chase the wire from the relay to the pump and check it along the way for voltage. i noticed on mine, when you first turn the key on, it pulses a few times iirc. iow, it doesnt give constant 12V to the pump. make sure you're watching for that.
on mine it ended up that the pump ate the prefilter sock thing.
'90 YJ, ford 8.8, SOA, lincoln front, aussie rear, 4.88s, swampers.