Yeah, Adam is well aware of the tuner hole issues. The problem stems from the templates in the factory and we can't seem to get it completely rectified. Some are certainly better than others, but it's always a bit of a dice roll. Most people dowel and re-drill them if they are particularly noticeable, they often only have to move less than a mm, so the dowel is easily covered when the tuner is installed.

It's annoying, but its also a trade off on the kits being so cheap.

And re the neck. If you've got it straight enough to fret level, then it should be fine and will settle once strings are on. I'd expect a bit of messing around at setup time.