Hi Jeff :
First off, I'm usually on the ST1100 side of the Forum, but took a look at the ST1300 side tonight and spent about 30 minutes reading the posts on this thread, your responses most closely. So, please accept my condolences !! You have one heck of a very interesting problem. I would hate for you to sell your ST1300 and admit defeat !!
I got a little excited looking at the scope tracings, being a retired EE and electronic tech with about 20 years experience. That narrowed the possibilities, since ALL coils & injectors are affected at the same time. And it was nice to see those steady crank position and camshaft position signals.
My guess is that there may be a bad connection on a connector, pinched wire at a crimp connection that is intermittent at that narrow RPM range ( I have seen this before, only at a certain vibration frequency ), OR an intermittent open IAT sensor.
I have seen connection pins that looked nice & clean, but when the connector halves are pushed together, the contacts don't make a good connection because a pin isn't seated fully into the connector. In fact, I had a problem like this on my ST1100 which caused an intermittent starter button.
Also, a friend of mine had a real interesting intermittent problem with his K75 BMW years ago. It would cut-out and then restart OK. It would happen randomly ( not repeatable, like your problem ) usually weeks apart. Turned out to be a flaky IAT sensor. When the sensor opened ( a thermistor, so an open would simulate a very low temp ) , the ECM was programmed to shut off the ignition ( ??? ). A new sensor cured the problem. I guess it's feasible you could have an intermittent connection inside the IAT only at a certain vibration frequency, or a flaky connection between the IAT and ECM.
Just for S&G's it might be worth unplugging your IAT while the bike is running and see what happens. Same for the coolant temp sensor.
I'm betting on a flaky pinched crimp connector or flaky connection at one pin at a connector that goes to the ECM, if the IAT and CT sensor checks out OK.
Good Luck !! IMHO, You have too much time & effort invested to sell the bike.