Set the STV position sensor to open sooner. Btw, the K7+ sensor reads 1.08 - 5.05 k-Ohm across the black and yellow circuit. Setting the closed value as close as posible to the 1.12 k-Ohm recommend in the book for the main TPS yealded 5.08 while fully open. Which happens to be what the open (reference?) circuit value is when testing the black and red wires. The bike starts and idles fine so I'll call it a win. For reference, the original values were 1.62 - 5.58 k-Ohm and the valves are positioned at 2.13 k-Ohm after the startup sequence.
Next, I mechanically checked the synch of my main throttle butterflies. Oh man were they off! No wonder I've had such bad engine vibes. So I mechanically synced them and will fiddle with the air screws next to try and even it out as much as I can without being able to lock the ISC valve.
I found out that you can't just disconnect the output tubes and tape over half of the hose opening. That experiment failed to the tune of a 2.5k rpm idle speed. So clearly there is a lot of restriction going through the ISC.
EDIT: I think I cracked it. I pulled a page from the FJR book and reset the air screws. I screwed them all the way in, marked the position with a sharpie, and screwed them both 1.5 turns out. Next, I balanced the throttle plates with the engine at speed, ~3.5k in this case. Finally, using the air screw on the rear throttle body only, I set the balance at idle. Twisting the rear screw had opposing effects between the TBs. The reading at the back would go down while the front came up, and vice versa.
The results were reduced vibration at idle as observed in the mirrors and hand grips. Also, cruising anywhere from 3-5k RPM was buttery smooth with noticeable vibes starting at just over 5k.
I'll be redoing everything to get the sweet spot from 4.5-6k if I can. Then my normal highway use should be nice and smooth.