The letters are the plug and location of the pinouts on the ECU.. such as connector B position 10, connector C position 1, etc. They are most likely going to be in different locations with OBD1, but you'll have to get the ECU pinouts (available on this site) and check to see if all the wires are routed correctly.
If you don't have an injector pulse your ECU is probably not receiving a crank position sensor input, cam position sensor input, or the ECU may have a problem itself. Check into those things first.
Definitely do not start moving wires around to the ECU unless you are absolutely sure you're putting them in the correct location. One wire in the wrong position, depending on which one it is, can destroy the ECU.