I don't see a fuel injector relay in the wiring diagrams. However the injectors are powered through the "main relay", which powers a wide range of other functions as well. (It's a large relay, with 6 connections.) I would tend to doubt the relay as a problem unless I've already established, through measurements, that it's faulty.
The injectors (all four) get 12 V through the relay. The other side (electrical) of the injector wiring goes to the ECM, and is grounded there momentarily by the ECM to cause the current to flow through the injector solenoid which opens the spray valve.
Have you checked for power at the injectors? With one or more of the two-wire injector electrical connectors disconnected, and the key at ON, check for Voltage at one of the two pins -- I believe there should be at least 10 V.
Then with the injectors connected, have someone crank the engine while you listen with a mechanic's stethoscope at each injector. If the injectors are being pulsed by the ECM, there will be a distinct click as each injector is activated and released. If there's a click the injectors are working. If there's no click, the ECM isn't triggering the injectors. It's not likely a fault in the ECM; rather, and in light of the fact that you were working in the engine/tranny area, it's possible a connector is off in the wiring harness system, or the wiring to a sensor, such as at the crankshaft, is off, and the ECM is preventing the injectors from firing for good reason.