Hi and welcome to the addiction! Here's my thoughts, not stone carved by any means:
1) - First and foremost, find the centerlines on both the neck and the body! When you know that, you can clamp the neck in place for further adjustment.
- Most likely you'll need a wedge shaped shim if the cavity and heel are true to Fender specs. You don't know until you have the bridge to measure with. A long metal ruler as you mentioned in the video is the right tool.
- I don't think the small angle would matter significantly even if you attach the neck before shimming. After all, there ought to be some wiggle room in the screw holes of the body so that the screws only grab to the neck when tightening.
2) - I wouldn't use anything other than wood for filling the gap in the neck pocket, especially not with expensive woods.
- Again, wait until you've got the bridge. There's a slight chance that you only would need to fill the short cutaway side of the pocket but you can't tell until you've got the bridge.
- With the bridge in place and the neck clamped you don't have to string it up, The two E-tuners in place you can use basically anything starting from knitting yarn or sowing thread to align the neck with the bridge. You can even use a small line laser if you have one! Or lay a long straigth edge ruler flat on the fretboard with the edge on the string grooves of an E string at both ends, repeating for the other E string line. No matter what you don't need to tension the makeshift strings more than what's needed to keep them straight.
As with any wood, sand with a very light hand. Only let the chips of the sandpaper dig halfways into the wood so you'll have space between the grits for the dust. And dedust your paper often.
If you're worried about the drill cracking the wood, start drilling backwards! That prevents the bit from chewing into the wood and splitting it. Lubricating the screws is good practice, all you need to do is to turn the screws into wax or soap, that will make the threads slick enough. Any semi soft wax or soap will do - table candles can be too brittle but graveyard candles are perfect! Although beeswax would smell nicer...