Per the FSM the only misfire/rough idle/stall after accelerator pedal depressed matches are:
Volume Air Flow Circuit
Injectors
ECM
Spark Plug
EGR
The EGR is ranking pretty high in priority per the FSM across all 3 symptoms. How did you disable the EGR system?
Fuel Lines and Fuel Pressure Regulator do also line up with rough idle and stall after acceleration. It seems you need sst 09268-45012 in order to check fuel pressure. There's no test for the regulator on its own according to the fsm...[edit: if pressure is high, replace fpr seems to be the test. If low, check fuel hoses, fuel pump, fuel filter, fuel pump relay, fuel pump resistor, injectors]
Are you sure you found any and all damaged wires while you were in there?
Sucks man, hope you get it sorted.