The '99-'02 rear hatch houses the keyless entry receiver, which also controls all back door functions (and communicates to the body ECU via an early-style not-quite-CAN bus).

With the rear ECU unplugged, the main 4-doors should still lock when pressing the driver or passenger lock buttons, so I suspect there is still some issue up there.

The alarm will not activate if the body ECU does not receive the 'ok' signal from the position sensors on all 4 door locks and the rear hatch lock via the communication bus (nor will the single-beep activate on non-alarm trucks).

Since the rear window works from the dash button, the communication bus is working, so that's a plus. I'd track down possible issues in the driver's door harness and/or master switch panel. There may have been a related issue that happened up there at the same time.

-Charlie