I am working on my first commission right now and those types of thoughts have surfaced every time I've made a mistake, really. This is a set neck and I accidentally routed the neck pocket about 1/64th too wide, and when I found that out, I got really upset and had to just step back for a couple weeks. Then I ended up shimming the thing and all is looking good, but I definitely know what you are talking about.
As far as builds for myself, I have cut up and tossed out two so far because they simply are not up to the standard I want them to be at. The really tough thing is that I work with lots of guys who love guitars, but don't build them. So when they see one of my builds, they tell me it's awesome and such, but I have to resist pointing out mistakes and stuff because I think that we hold ourselves to a really high standard as builders, even higher than lots of guitar enthusiasts. In the end, I think it's like my dad always said, the secret to woodworking is knowing how to hide mistakes and not tell anyone, because you won't have a perfect piece.