Hey, I know exactly what that feels like. I am writing up and the whole time I am finding experiments I should have done differently...why did I do x at pH 6, when pH 3.5 would have made more sense? Why did I incubate at 40 degrees, 20 degrees would have been more logical? I just console myself with the fact that a PhD is meant to be a learning experience. If you can see when your work is not perfect, and why, it is a sign you have learnt from the experience. Don't despair - just do the best you can with what you have and know you are not alone in feeling like you are the only one in the world with a poo project. Good luck.