If the ECU receives all the correct signals and is functioning properly, then it should energize the EFI system (fuel pump, injectors, O2 seonsors, coils,etc) properly. A pulsing signal would indicate either a faulty ECU, or one or more errant intermittent signals to the ECU, or perhaps faulty wiring (shorts?). Is the ECU/EFI light illuminated? Bad ground? Low voltage? Voltages correct? Failing relay?
Do you have a PDA for this system? If not, it may be worth having the dealer hook one up for diagnostic purposes.