I was also thinking his fear of the counter may be due to his toes, lack of balance, as counters are slippery and he knows this from being on them before, so maybe put some of that non slip stuff you have on the window sill, as he seems comfortable with that surface.
Try to see if you use it in different areas that he use to go to, if it makes a difference. As far as the food, i have no idea other than the clipping threw him off and he is doubting everything most of all himself but that will change back.
We have had to clip a couple of ours before and after a few days they readjust. Their normal routine slowly creeps back in.
All the best and keep us posted as we are all rooting for all 3 of you.