We are having a similar issue with a 1J into a pre-89. Did the 12v mod and the pump runs when B+ and Fp jumpered in diag box (check connector) with the Ign Switch, but not when those signals are jumpered at the FP relay instead (like the 12v mod calls for).
Am looking at page FI-70 in the TRSM and it looks like the Circuit Open Relay is the culprit, but means that the Fp signal/circuit is not making it thru the COR to the Fuel Pump Relay. So, we are looking to bypass the other relays anyways and just jumper the B+ and Fp somewhere other than at the FP relay.
Will be troubleshooting the circuit open relay today, to see if we can find the real issue, but we at least have the alternative above.