The only mod I had done when I picked up my Speedmaster last year was a set of floorboards. I'm on the tall side and prefer the flexibility to move my feet and legs around a bit. I've done several mods since, but if I had it to do over again, I'd start with a swap to progressive springs in the forks. That mod made the single biggest difference in the fun factor, and it's not expensive. The stock springs take such a dive when braking hard that it made the bike hard to handle and I was always anticipating the next hard stop and what could happen. Swapping out for progressives takes the drama out of the next braking event. Anyway, if I had it to do again, that would be done before it left the dealership. As for most of the other stuff, I'd recommend riding for awhile to see what bugs you, find out what other forum members have done to address the issues, and go from there.
Gary