Firstly I noticed on the megastim again, that fp dimly lights when the fidle circuit goes off. Then while on the stim I tried setting the temperatures way high to see if fidle went off, and it did, so it'd warm up then stop working like you suggested.
I went over the pcb and no shorts around the pins or traces between the two circuits and all the components associated checked out apart from the transistors which I couldn't test in situ, so I went for broke and desoldered the two transistors, and soldered the fidle trans into the pump circuit.
Result? I now have a working fuel pump output. I'm guessing the transistor was bad, maybe I have issues with the megastim too and the crosstalk was coming from that instead. Ill order some more transistors just in case, they don't cost much. Thanks for your help.
Case it back up, get tacho out + a shift light working then go over it with a hot melt glue gun now