Robert,
Sorry, I guess I shouldn't have been so adamant about not using HW store parts. To be honest, there are probably not that many instances where an out-of-tolerance bolt is going to get you in trouble. I mean, if the bolt is too big for the hole, most people are not going to go get a hammer and drive it in, so my advice is unwarranted.
I really just wanted to make the point that reusing AN hardware is not really a problem, as some people would have you believe. When test fitting parts, you really should not be final torqueing things, so there should not be a problem with ruining parts.
One thing that I always do is run a screw into all nutplates, either before or after I install them. This is just to make it easier to install screws later. I use the same screw for all of the nutplates, and I do not throw the screw away afterwards. Obviously, this one screw probably gets a little overworked, and maybe it will not be as good as a fresh screw. However, there are no places where the airplane is being held together with a single screw in a nutplate, so I doubt that this is a problem. Of course, if the head gets mucked-up, it needs to be tossed. Also, if you can insert the screw into a nutplate with you fingers, then it is probably hosed, and should be discarded.
However, I would never use a non-AN screw to clean out nutplates. A nutplate has been squeezed just slightly in order to be a reusable fastener (works like a nut with a nylon insert). You do not want to put an oversized screw in it. Also, I don't think it is a good idea to use a tap on a nutplate in order to get a screw to fit easier. I know Van recommends that you do this in a few places, but a tap will remove metal. In my opinion this defeats the purpose of the squeeze on the nutplate, and I would not do this, unless I had a nutplate that was just way out of spec. I have never had a nutplate that is so tight that running a screw in it will not ease it up just a little. BTW, I forgot to mention that I drag the screw in some Bolube first.
Of course, I am not a mechanical engineer, so this is just my opinion. Note, that opinions are like, well, you know, they are worth what you pay for them.
Cheers,
Tracy.