Well I have good news guys! Everyone was right!
I found the main side rods on the rear powered unit to be grabbing intermittently due to sloppy tolerances. The would slip in and pinch between the wheel and spacer (which they were supposed to be on). This only happened under certain conditions so it was tricky to find! The teeth that engage with the wheel were too large and wouldn't fit in the slots intended for them. I filed the teeth smaller and that solved the binding. I missed that the first time I investigated the side gear.
Also with an oscilloscope I watched the engine run with the old controller still in it. I saw a lot of shooting through (big current spikes) for no apparent reason. My best guess is the triacs were sticking open. Good reason to not use triacs for motor control. The cruise commander M I installed uses PWM like the Legacy engines do so it runs like an absolute dream now!
