I could be wrong about this, but I believe that if you've got fuel and spark, the ECU is at least partially working. Have you verified that the engine timing is correct? With correct engine timing, fuel + spark + air should = a running engine. Try to get a second opinion on the OBDII scanner, just to rule out whether or not your scanner is at fault. Maybe borrow one from a neighbor or have Autozone or Advance Auto try and read it for you?
EDIT: It's a '94? And you actually have an OBDII port under the dashboard? I thought that OBDII was for 95+. If you've got an OBDII scanner trying to read an OBDI ECU, you won't get anything. I'm not even sure if there's a place for it to plug in lol
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