It can still be fuel related. When the computer goes into limp mode, it runs in a preprogrammed known mode that will not damage the engine and allow it to keep running, just not at optimum performance. So it could be running on a cal that allows teh injector dwell to be large enough to compensate for the low fuel pressure. This is all speculation at this point, and if someone knows better please chime in. One way to tell if the pump is doing it's job is to pinch off the return line with a gauge on the rail, the pressure should go over 70PSI if you pinch it off all the way. Are you sure you connected all of your grounds back up, and they are clean. Also it wouldn't hurt to do a tap and wiggle test on all your connections. Might have a pin push out in a harness somewhere, or rub through on a wire.