Did you ever bore your throttle bodies? Like told them a long, dull story?
I did. 58mm ID/56mm ID top to bottom instead of 55.5/52 stock, then hand blended the 56 bottom into the rubber mount. I netted no meaningful result from it at the time, but, I now believe I've been hitting a flow limit at the exhaust valve, completely negating the gains from the TB/Nev's Cams/etc I'm working on solving that, I have a head at the shop getting some work done now for 40 intake / 34 exhaust valves.
One reason I suspect this to be the case, is a dyno sheet I found from a few years back. With 4" stacks and with stock stacks. The 4" stacks gained 7lbft everywhere below about 6500, and the two setups were within 2 hp up top, the short stacks should've pulled ahead up top, they did not indicating there's a flow restriction elsewhere and valves are the only remaining possibility.
On ECU Choice
I've tentatively settled on the MaxxECU Race Hydro as my ECU. Having an EGT sensor per cylinder is something I do want and having it built into the ECU is nice. The MaxxECU Race has more flexibility and features than the Motech or Haltech while sneaking in at about $1k less money and can play nicely with almost any CAN device on the market since it has it's own CAN sniffing/decoding functionality built in to the ECU.
So the full setup will be pared down to mo.unit blue for chassis harness control and ignition circuit control, MaxxECU Race Hydro for engine management, and Haltech IC-7 for Display. Bosch 2in1 Temp/Pressure sensors for oil/water/fuel. Triumph sensors for trigger/speed/wheel speed/ etc, KTM throttle tube, R35 GTR smart coils, and the BMW ITB Actuator controller. Cam position sensor is going to be attempted using a cam lobe as the trigger, if that doesn't work, I'll go to a single tooth cam gear modification.
A less ambitious conversion could be done with all stock sensors, gauges, vehicle harness and simply swap the MaxxECU, KTM throttle tube, coil igniter, and BMW ITB actuator for a DBW conversion for around $2750 to give 1 gen Rockets full traction/launch/engine control/cruise/multimap etc. Without the cam gear it will run in wasted spark, but if my cam lobe as the trigger mod works, it's trivial to get full sync control.
Edit:
I just found a key feature applicable to R3s... Cam position trigger is the biggest hurdle for this engine configuration, well..MaxxECU have a MAP based home trigger and configurable MAP pressure threshold. When Cylinder 1 is on the intake stroke it will spike that MAP signal and the ECU knows that #1 is on intake, then compares that to crank position and it gives a means for full sequential engine control without an extra cam sensor. BAM, Maxx wins the best for rocket 3 feature set with that alone. This is the Keihin home signal strategy used by the stock ECU and maxx the only fully compatible standalone with the stock hardware.