#1 - I'd play a bunch of different "hard-tail" guitars to find out what bridge you like. I'm partial to the Bronco/Musicmaster Vista model tailpiece for hardtail myself these days when it comes to offset-style guitars, I tend to find on the Jaguar/Jazzmaster, a bigger baseplate hardtail is better for aesthetics as you will have a nice chunk of wood down there with nothing present.
#2 - My experience with Yamaha pickups has been good, I had a Pacifica 112V for a few years that I liked the sound of, I think it had the same pickups (2 alnico 5 single coils in the neck and middle, and a humbucker in the bridge). I like the sound of the Squier 51 humbucker. If you are changing pickups, and like resonance, a swimming pool route might do you good with some careful planning. You could even set it up to where you could upgrade to a full-blown Jazzmaster pickup set later as long as you mind having a "shelf" to screw the pickups into.
#3 I'd say consider your sound and what you want to sound like. Jazzmaster pickups are not single coils in a P90 bobbin though, they are more like squashed-flat Stratocaster pickups. The sound is typically very sizzling in the treble department, almost acoustic-like, with a warm low, and they are very good at cleans, and backed off or with 500K> pots can get near P-90 territory.
If you do HSH, you likely won't like the result of the pickup selection using default Jazzmaster switch. You will want to use a 5-way switch at least, or 3 individual switches like a Jaguar (one for each pickup). If you want coil tapping the 2nd option is the cleanest and more logical in layout.
