It's great you got your half scale length spot on, but just remember the overall length is the critical measurement. Your 12th fret measurement can be 1mm long or short and can still intonate correctly when you're done. I always go by the full length measurement as my final target.

To my eye (could be different IRL) the neck alignment looks like the treble E could go a tiny smidge inward, but you're not gluing yet so not critical right now. At least you have an idea of the fit at this point and the alignment won't be an issue.

Whilst the results vary according to the wood type, grits above P240 can start to burnish the surface of some woods in patches, especially if pressed down with some force, resulting in uneven stain take-up.
I agree that variations in timber are a consideration but FWIW, I've not had an issue using 400 before stain on Mahogony, Maple, Basswood or Ash. Maybe because I am light handed with it, or maybe I've just been lucky.

Worth noting that I've not encountered adhesion issues with the clear coat after either, but TBH most of the clear over stain I've done has been hand applied so that may make a difference there.