Today I removed the secondary butterflies from the throttle bodies, opened up the airbox completely and re-set the TFI to Dale Walker's Stage II settings. What a difference - completely smooth, spools up and down faster, better throttle response and feels like it should.
Stage 2 is the TFI, secondaries removed, PAIR plugged, BMC filter, Yoshi TRS, airbox opened right up and O2 sensor bypass. Wow.
I haven't dynoed it, but Dale's extensive work shows the chart below. The bike should be producing around 122 hp and 92.4 ft-lbs of torque. Big fat gains right through the range and it feels it. Max torque kicks in at 6,000 rpm. At 5,000 rpm, that's 90 ft-lb, which is better than a B King at those revs.