ive seen this happen on a focus it ran sometimes then it would just cut out and not start for a while ended up the thrust washers were fucked .

you should if there is any play on the pulley on the timing belt side first before you pull the box out .

if i were you i would see if you could get your hands on a different cps or even try yours in another car it would probably be the same as any efi cvh out of an escort or orion or fiesta.

did you check the continuity of the wires back to the ecu ?