Did you put the right pump? Bat has a return type and a returnless.
Return type: Fixed speed (fixed voltage, constant output)
Returnless: Variable speed (Varying voltage, varying output)
The returnless pumps vary speed to vary pressure. The earlier systems used a mechanical pressure regulator.
If the pump is putting out too much pressure and not varying, you could be over pressurizing the rail, causing the sensor to read a presuure higher than it can read.
A guess, but if the pump is staying at one speed, and the PCM lowers voltage to lower pressure, the pump, instead of slowing, may cut out at the lower voltage. Then when the pressure drops, the voltage goes up, the pump comes back on full speed instead of a lower speed and overpressurizes the rail.