Well... I think I'm going to throw this thing in the can. I removed all other variables that may affect power, and tried to power my Pi as directly as possible from the MP2636.
However, it appears not all MP2636 are created equally, the new one I just modified tonight behaves radically different from my last module.
I am seriously disappointed in this unit and very much disheartened by months of failure.
I no longer think ANY portable Pi is possible. The Pi simply uses too much power. On the bright side, powering via battery works amazingly well, even manages to run cpuburn on all four cores no sweat (until it gets over 82°C at which point it thermally throttles on me) as long as you don't use the official raspberry pi power supply - plugging that in to charge the battery causes a high pitched whine, the screen starts distorting and the red LED goes haywire.
Time to find a use for all this junk now