Just to add another data point: My Capo's VIN ends in "000296". I picked mine up in April of 2002. I also received the sidecases free as part of the "First 100" promotion. Go figure. :-)
As for the stalling/stumbling problem, early on my Capo had very minor symptoms. After the first service (done at around 800 miles), it was pretty much gone. The mech said he synched the throttle bodies, though I can't say what tool (electronic or otherwise) he might have used. Now at 8K miles the bike continues to run great.
Also FWIW, when I first replaced the check valve (as described on Todd's site) it was done to relieve the severe negative pressure building in the fuel tank. The vacuum was strong enough to make opening the gas cap a challenge and noticeably suck in the sides of the tank. I suppose concluding it was connected to the low-rpm stumbling problem might indeed be a good example of "internet science" on my part. :-) However, for two bucks it's easy to try and it definitely cures the vacuum problem in the fuel tank.
rgds, Marty - 02 Silver Capo (#296!)