Are you getting power at the coil? I'm not sure exactly how the system works, but my guess is that with the key in the run position, you should be seeing voltage going into the primary (low voltage/12V) side of the coil, and when you turn it to start, the ECU is gonna open that primary side, thereby inducing a voltage into the secondary (high voltage) side of the coil and then once the engine's up and running, the ECU is gonna see that the engine is turning via the crank sensor and keep triggering the coil same as if you were trying to crank. Just because you replaced all the fuses doesn't mean there isn't an open somewhere else in there... You said you replaced all the wires, what about the actual coil-to-distributor wire? It definitely sounds like it could be the ECU, I'm just trying to help you cover all the bases before you go shelling out more money for one of those.
Edit: I should add when you check for voltage, use a digital multimeter. The wiring diagram I have says the coil/ignition module isr wired into the ECU and analog stuff can screw up computer circuits. Also, now that I'm looking at my Haynes manual, it might be something in the fuel system or the emissions system. There seems to be a yellow wire that runs from the ignition module to the switching side of the O2 relay and also to the control (looks like ground) side of the fuel pump relay.
here: