Hi and welcome.

Best to start a build diary and ask technical questions there as that section gets more attention.

But...

1) Yes, for fret levelling you want the fretboard as flat as it can be. But you may not need to level the frets unless they are all different heights. But until you get the fretboard level, you won't be able to check this. This is where you really need a notched straight edge (the notches fit over the frets so the straight edge sits directly on the board). You can make your own, but they don't cost too much to buy. And one is always useful for checking other guitars. You'll almost certainly need to give the frets a polish, but you may not need to level the frets. It's something that can happily wait until the guitar is assembled and you see how well it plays. Unless there are definite high or low frets, you may find that a fret level only improves things by a very small amount.

2) It's done happily both ways. I leave small holes until last as it makes wet sanding easier. Water will get in the holes (unless you fill them with wax or similar) and can swell the wood and split the finish.

What you must do is ignore the guide for setting the bridge position where it says set the saddles
In the mid position for measuring the scale length. Set the saddles almost all the way forwards, as they will only come backwards from the scale length position when intonated.