Wow. While not a huge JM fan I love what you have done to this one. The pau ferron board looks beautiful now that you have scraped it and I like what you have done with the electronics. I had always thought that a 250K volume pot would work better - Jazzmasters can be ridiculously bright.
Andare - I like the arm in my Strat to be as low as possible where it comes out of the block. I don't like when there is a length of the arm sticking out of the block before the bend - it really affects how the arm feels to use. The vintage vibrato arms are much better in that they are mounted at an angle into the block. The newer versions where it comes out at 90 degrees are nuts! You have to remove them from the guitar every time you put it away in the case. I like how the old ones can just swing around close to the body when storing.
I have a set of taps and dies I bought very cheaply from an auto parts store. I bought it for working on my motorbike but found that one of the dies is exactly the same size as the thread on a Strat whammy bar. So if the bar sticks out too high I can just thread it a bit more to screw down further into the block. Sometimes I'll need to cut off a little bit to let it fit. Then I use plumber's tap on the threads to help it stop wobbling. It makes a huge difference.