If you have access to a machinist, that could be good, just need to find out the specs of the type of portwork you want. Generally, just a good machinist and powered handtools are what does the job.
As far as the pipes, it should be reworded that the SST's don't respond AS well. They will respond in a positive way, it's not like the bike will run bad. it'll run much better than it does now, however, the possible gains could go up with a set of pipes that respond better, make sense?
I'd port the cylinders and keep the SST's and see how you like it afterwards. Down the road, if you think you'd be better off with another set of pipes, deal with it then, but you'll get some decent gain out of the SST's with portwork, for sure.
Rejetting is not necessary when advancing the timing, it has no effect on air/fuel ratio going into the motor, just when the spark occurs. Boonman can lighten the flywheel if necessary and mill the head for more compression if need be, but sounds like you have a good set of machinists there that could mill the head for you.
Scott