Bueller went for lunch.

I *think* that the ECM supplies Ground to the fuel pump relay. As in, the relay gets its 12v from the battery and then the ECM grounds the other side of the relay coil and the relay engages. This is an electronic design trick to limit the juice to be supplied by the ECM, instead, it just has to pass the juice back to the frame (ground).
I betchur ECM is not supplying the ground on pin 22. Seems the ECM may be defective.
It is a little late, but you should have checked the part number, build code, brain fade on the term but it is the emission "batch" level, as you may have gotten the wrong one from your supplier. I would also check the fuel relay amp draw by taking the ECM out of the circuit and supplying 12v and ground thru an ammeter. It shouldn't take many amps. And, it shouldn't get hot or smoke.
THe time thing to me indicates something is getting hot, (or was) and an electrical connection, perhaps a winding in a relay, was opening up and de-energizing your fool pump.
tom