I recently defended my PhD thesis and was awarded a pass with some minor corrections. I am due to submit the final version of my thesis in 2 months time from now.

The examiners were both very happy with my thesis, which explains the final verdict. However, as the saying goes, no one understands a thesis better than its author, as he/she is the person who was invested in it for years. When polishing the papers to send for publication, my supervisor and I found a major issue with the thesis, which although it does not invalidate the overall results, it would change a significant portion of the methodology in my thesis. While I am currently addressing these issues for publication, it has to led to severe depression and has made me feel inadequate as a researcher. I worked incredibly hard and had a particularly difficult PhD process; so it is difficult for me to find that at this stage (post defense) I am submitting a thesis that is predicated on a methodology that should have been approached enirely differently. This in turn has caused a feeling of despair and inadequacy.

I spoke to a friend who is now working as a associate professor and he comforted me by saying that irreproducibility, inaccuracies, and mistakes both major and minor are very common in PhD theses and that I should not beat myself up for this and that the said PhD title is well deserved. However, I thought I ask for some second opinion.

Definitely OK. Mine was pretty crap in my own opinion. The PhD is an apprenticeship in research (that's how I view it anyway), not your lifework or the best work you will ever do. Pass with minor corrections is a great outcome.

Something that could help might be to list the inadequacies of the research as you now see them. And also list how you would address each one / do it differently. That way you are learning from your experience and making something positive from it.

Maybe you could seek to address your feelings in different ways - like really challenge your thoughts that are taking you to that place. By the sounds of it you have done fantastically and are doing fantastically (recently passing the PhD and now polishing up papers for publication doesn't sound like being an inadequate researcher to me). Congratulations!