obviously the last sentence of my post should read 'ask *your* supervisor'!!!

Guidelines are there for a reason - and yes, they will reject your paper if it is too long, or tell you to cut it down. 7000+ words is MASSIVE for a paper. If you have 7.5 pages but over 7000 words, your paper is clearly not in the correct format. Ask our supervisor for some guidance on where they think you could afford to lose some words.

If the information is something that is 'common knowledge' in the field, then that does not need to be cited. For example, if you were to write 'the heart pumps blood around the body' then that would not need a citation as it is such a well established fact. Therefore, things you learnt at undergrad may not need citing if they are ideas that have been commonly accepted into the literature. Have a look at some other examples of papers in your field to see what I mean - not every single sentence will have a citation. If you are using other people's work from conference presentations etc., then you will need to cite these. Although it is a pain checking all the citations, it will be good practice for writing up your thesis :)

Yep, I agree that this is definitely something you can work on and improve :) and please don't worry about your accent - in academia, you will come across people from all over the world, and I can guarantee that most of them won't even notice you have an accent! Non-native English speakers generally can't distinguish between English regional accents (unless they find you very hard to understand!). I have been to conferences where every single speaker has an accent, whether that be non-English or a regional UK accent, so you won't stand out in the slightest.

Like anything, the more you practise, the better you will become, so stick at it and it will get easier. Even if you just present out loud to yourself at home, this will help you become more confident. Use flashcards to remind you of what you want to say about each slide if that helps, as it may stop your mind from going blank. I get very nervous about presenting, but I get told that this doesn't come across, as I work really hard at putting on a confident front even if I don't feel it. Smile, breathe, and take your time, and the rest should come naturally!

The quote buttons aren't always there! If I am reading a thread without logging in, and then I login to reply, the quote buttons aren't there. But if go back to the home page and then back into the thread, they appear. If I login from the home page and then go into a thread, the quote buttons are there straightaway. Minor niggle, but annoying!

Working from home really suited me, as I liked the 'hands-off' approach that my supervisors took with me. If you are the kind of student that likes the extra support, then don't do it, as your supervisors are very unlikely to give you the same support as they give to people that they see every day. But I enjoyed being left to my own devices, especially as I didn't feel so pressured to stick to specific working hours. For example, I often took a day off in the week to go shopping, do things related to my hobby etc. and would then make up the time on other evenings/at the weekend without feeling like anyone was tracking what I was up to.
It can work really well, but I think you need to have a good plan set out to show your supervisor, so that when they raise concerns, you can show them what you plan to do about them. For example, if they say you won't have enough contact, agree to have weekly phone calls and monthly face-to-face meetings (or whatever you think is necessary) to prove you will still be committed. Or you could agree to send them a weekly/fortnightly update of your progress so that they can see what you've been doing.

I think all the issues you raised are very valid, and should be considered carefully before you raise anything with your supervisor.
I did most of my work from home in my final year, as I lived about an hour away from uni and it was just a pain to go in all the time when I really didn't need to (my project was computer-based). However, they definitely 'forgot' about me to a certain extent. I didn't get a chance to really socialise/make friends with my fellow students, which wasn't important for me in terms of my social life but did make me feel very out of the loop. On the odd occasion I did go into uni, it was weird to not know anyone and feel like a stranger in the department.
My supervisors definitely gave me much less attention than they gave to other students, and if left to them I would go months without any contact. I made an effort to keep in contact with them so they were updated with my progress, and we met face to face once every 4-6 weeks if possible.
For me, this wasn't such a big deal as I didn't want to work in academia. However, if I did want to do a postdoc, I wouldn't have fancied my chances of getting one in the department, as other students were definitely favoured over me.
I did some teaching in my last year, but for a private healthcare company who ran workshops for A level students. This was right next door to my department, so I if I was doing teaching there, I often had to hide if I saw my supervisor so they didn't ask me why I wasn't meeting with them at the same time!
Continued in next post....

PS. I should also have added: don't get disheartened if your paper gets rejected! It is very common for papers to be rejected first time, so take on board the reviewers comments and keep trying!

Publishing in a journal is quite different from writing your PhD, mainly because you are restricted in terms of structure, word count etc.
The best place to start is to pick which journal you are going to submit to BEFORE you start writing anything. This is important as each journal has different rules so it is really important that right from the start you know exactly what format and word count you must stick to. Even little things like how they like you to write units can be a pain to change at the end if you suddenly discover yours are all in the wrong format.
In addition, once you have selected your target journal then I recommend reading a few examples of papers they have published recently, so that you can get a feel for how they are written in terms of language, flow etc.
If you google 'writing for an academic journal' there are lots of useful guides out there from various universities that should help.

So if I have understood correctly, the work he is questioning isn't related to your PhD and hasn't been published? If so, then a case of scientific misconduct really won't have much basis. However, I agree with Mackem_Beefy that it would be a good idea to prepare yourself in terms of how you would defend yourself against any such claim, i.e. do you have any lab books, records of what you did etc? Other than that, I would say just sit tight and ignore him, chances are he'll go away as it doesn't sound to me like he has much of a case to do anything with.

My advice is: expect it to be a very difficult and long-winded process, and then you won't be disappointed! I did manage to get a paper published during my PhD (I was in the sciences) but it was painfully complicated and depressing.

I was at the start of my second year when I first sent the manuscript off to a journal - it was rejected after about a month, and the reviewers were pretty harsh (well, 2 were fairly constructive and 1 ripped it to shreds!). So I rewrote the manuscript based on this feedback, and resubmitted. This wasn't as easy as it sounds, as there were four co-authors to please too, so this took months of writing and re-writing multiple drafts til everyone was happy with it. Eventually, I sent the manuscript to a second journal. This is where the fun began, as I am pretty sure they completely forgot about me and it took nearly a year of almost constant pestering before they decided to review the manuscript. Eventually, after another month, they provisionally accepted the manuscript subject to me making a few changes. So I did the changes, got them approved, and finally, more than 2 years after starting the process, my paper was published! Fortunately, it was published about a week before I submitted so I could fully cite it in my thesis, which was pretty satisfying!

I now work in medical writing, and deal with manuscripts from top experts. They too get their manuscripts rejected and ripped to shreds on a regular basis, so when I realised that it made me feel a bit better! It is very rare for a manuscript to just be accepted at first attempt.

So sorry for the negative tone to this post, I don't mean to depress you but I thought you should be warned about how arduous it can be! You might not have these struggles and your manuscript might be accepted almost straight away, but be prepared for it to be complicated and disheartening. And remember that this is completely normal, and most manuscripts get rejected at least once before publication.

If you have adapted the figures so that they are slightly different, then that is usually sufficient to circumvent the copyright laws (and reference them as something like 'Adapted from Smoobles et al 2013'). I write manuscripts for a living, and we often do this.
For example, if you are reproducing a barchart, if you flip it (i.e. make vertical bars horizontal or vice versa) and change the colours of the bars, then that is enough for you to no longer need to obtain permission to reproduce the figure. Or reproducing a section of a chart but not the entire thing.
If you want to reproduce the figure/diagram in the exact same format, then changing fonts, colours, labels, axes etc. is usually enough to get away with it. I reproduced a couple of figures in my own thesis in this way, be redrawing them myself in Excel/Powerpoint and just altering them a bit so they didn't look like an identical copy, and no one even mentioned them (obviously they were fully referenced too).

My PhD was in a subject I had never even heard of before! I saw the advert for it, realised that all the skills I had accumulated in my degree/masters fitted well, and applied for it. On my first day, I remember wondering what the hell I had done as I wasn't in the least bit familiar with any of the material, papers etc. However, after a few weeks of getting into it I really relished learning a completely new topic and immersing myself in something new. I never became truly passionate about my topic, but I enjoyed it and got a PhD out of it - it was means to an end for me, and I no longer work in a related field, but I needed a PhD to do what I really wanted to do.
So in my experience, it is possible to enjoy a PhD in a different field, and still feel fulfilled by the end of it. Just keep in mind your ultimate goal, and do your best to enjoy being able to study something different that you may not otherwise have had the opportunity to try!

I agree, 2.5 pages is too long - I would keep it to a max of 1 page. Your CV (which should also be as short as possible, 1 or 2 pages ideally) should have all the important info, and the cover letter simply picks out specific parts of your CV and relates them to the specific job you are applying for (as described above by HazyJane and bewildered).
I am currently involved in the recruitment process at the company I work for, and long-winded cover letters and CVs just make everyone groan :) Keep it short and to the point, or people will lose interest in reading it!

Firstly, LEAVING DOES NOT MAKE YOU A FAILURE! Sorry for shouting, but it's true - a PhD is not for everyone, but that doesn't mean you have failed in any way if you do decide not to continue.

Having said that, I'm not saying you should quit. It is perfectly normal to feel out of your depth for the first few months, and for none of your experiments/ideas to work out - even in my final year I still felt that the other students were much cleverer than me, had better ideas, had a better relationship with supervisors, were more likely to get things published, more likely to get a job afterwards etc etc... And I managed (to my great surprise!) to get a publication, pass my PhD with minor corrections, and get a full time job straight after. Even now I still feel a bit of a fraud, as if I don't deserve to have passed - google 'academic imposter syndrome' and you'll see that a huge number of people doing a PhD feel exactly the same way! In fact, there have been loads of previous threads on here about it.

Is there anyone at university you can talk to? For example, do you have an advisor assigned to you to help with non-academic issues? Or maybe a student counsellor? I think your anxiety/depression problems may be clouding your judgement, and you're probably doing much better than you think you are.

Best of luck, and please keep in touch with everyone on here - others will be along with more advice soon I'm sure!