Pretty simple. I've swapped between the 2JZ COP and stock coil setup twice now. The car has run the same with both setups.
Quick update:
The break up I had been experiencing at 3500 RPM was under very light load and light throttle (~25-35%). Against my better judgement, I decided to try giving it a bit more throttle to place greater load on the engine when revving to and past the 3500 range. With greater throttle (~50%) and load, no break up occured. This makes me wonder if it's tune related, to which point the engine is running extremely rich under light throttle. I suppose it could also be a boost leak. If all goes well I'll be installing a wideband O2 sensor tonight and can get a better idea of what's actually going.
I've been reading VF (Vf1 > volt meter > ground) and while adjustments with the MAFT create physical/audible changes in the way the engine runs, the VF signal seems to be unaffected. From my observations, the VF signal has five readings: 0.0xx volts, 1.0xx volts, 2.2xx volts, 3.5xx volts, and 4.9xx volts. The readings vary across this range, most commonly when either under throttle or lifting completely (goes from 2.2-4.9 while under throttle to 0.0xx when completely off the throttle). At idle, the reading has been any one of those five. Again, adjusting the Idle dial on the MAFT seems to change the way the engine runs, however the adjustments don't seem to have any direct effect on the Vf readings.