Hi, I'm new to this and need some advice guys. So I have decided to apply for a PhD and I now wonder what to do with references, CV and cover letter... :$

References
In some of the "how to apply" details it states " 2 x academic references only, whereas others is both academic and professional.
I graduated in 2007 with a degree in Physiology, then was offered work with my final year research project Supervisor til July 2008. I have since been working at a company contracted out by the NHS in a patient-facing role. My boss here is a Clinical Physiologist with a PhD himself. Who do I ask for references!?
I am guessing that both my supervisor from 2007-2008 and my current boss would be able to do this as both a professional and academic reference? Or should I ask my tutor whilst at uni (who I haven't spoken to in yonks!)?

CV
I am guessing this will be a standard CV but with more emphasis on my academic ability, grades, experience in research? Anyone got any specific advice? Have been looking on the web but all I seem to have found is postdoc stuff.

Cover Letter
Again, I am guessing this will be very much the standard cover letter but with more emphasis on academic ability, transferable skills, experience in research and what you hope to achieve/ future plans. Again anyone got any specific advice? Have been looking on the web but all I seem to have found is postdoc stuff.

Any input/ advice is most welcome! ,-)