The suspension has turned out to be pretty much a non-issue. Following my "This isn't a racebike" mantra, I decided to go with new front springs and rear shocks from Phil at Road & Race Motorcycle Engineering in Australia.
It's generally thought that raising the rear end of the bike using a longer shock will aid handling. I'm sure this improvement is real, however, if the shocks get too long, the centerstand will need to be lengthened too. Phil and others sell longer centerstand so that's not a big issue. But I was also worried about how it would look since the raising the back end makes the space between the rear tire and fender larger. Also... raising the back end would alter the angle of the chain and maybe increase the chances of the chain dragging along the case? (Steve at Bevel Heaven sells case savers to prevent this)
I asked around about shock lengths and found that you can only go about 1/2" longer than stock before you run into possible issues with the centerstand not working as intended. The stock length according to what I see in the parts book is 305mm. The shocks I was looking at come in 310, 320, and longer lengths. I agonized over what length to go with for an embarrassing amount of time before I decided to stick with what I knew would work - I ordered the 310mm versions. I haven't checked to closely yet, but from what I've seen so far I think I would have been fine with the 320mm set also (I'm running a 110/90 Avon AM21 Roadrunner rear tire by the way).
Someone suggested dropping the front end for the same effect on handling. Overlooking the slight reduction in ground clearance, this would work on bikes with clip-ons, but not my bike. There's no way the fork tubes can be raised up any further than the top surface of the triple clamp without hitting the bars. The bars look like they may need to be tweaked just a touch to clear the casting already.
UPDATE: Now that I've ridden the bike, I feel silly for having worried about this. It isn't a race bike. It handles just fine with the stock geometry. For cripe sakes, I have a 996 sitting around for times I want to pretend I'm fast.