OK Here I go foot in mouth probably wrong but I'm going with .......
Electrical ...
APS ECU ..............
Why cause thats what mine did when I had a problem (pre Haltech)
To prove - remove piggy back ECU, I assume this is safe I've done it with all mine, disconnect battery undo the harness from the APS ECU then the APS ECU from the OEM ECU and connect the OEM plug to the OEM ECU -
reconnect battery and start car - if it runs lumpy like it does when you're having problems (which is my guess) then I would think the APS is kicking in and out if it won't start at all without I'm probably barking up the wrong tree again, however as long as you don't fry the ECU it won't cost anything to try....???
Just a suggestion