Possible ECM distress 1989 Pontiac 6000 LE

I am going to try to give the short version of what is happening, one day the car desided not to start, during general tests for spark, fuel, ect. An atempt was made to pull up trouble codes, I used my home made jumper to activate code read, and when I turned on the ignition I did NOT get the usual code 12 fallowed by any trouble codes, instead the check engine light flashed on and off keeping perfect time and clicking was heard from underthe hood, when I poped the hood to inspect, I am guessing from vibration, "code read mode" began working I began getting code 12 but only 12, the cooling fan came on, everything seemed normal, I finished opening the hood, and "code read mode" malfunctioned once again, and the on off clicking noice returned which was in perfect unison to the on off flashing of the service engine light, the clicking was comming from the intake, (possibly the injectors)and from the electronicly controlled purge valve on the gas vapor canister. I jiggled wires under the passenger dash near the ECM as well as wires going to the code read jack, and at some point code read returned to normal, I assumed a short. I unplugged my jumper and started the car, she ran perfect for almost 2 minutes, started acting rough, and conked out, at this point, I could now hear the clicking noise once again from te engine area but this time very erratic and untimed.

the coil packs and module, inline fuel filter, air filter, oil filter, tranny filter, are all about 6 months old, the battery is about 3 months old, the starter soleniod is brand new, and we just replaced the ignition lock cylinder, and ignition switch, which we thought was the reason the car would not start or died not long after running because we did start havng problems with the cylinder and key, yet oviously as the problems I posted above, there is some other problem that is causing the issues,
one person suggested it may be the fuel pump, which I do hear prime every time, I turn on the ignition, and I do have fuel pressure at the fuel rail check valve,
another suggested it may be the injectors, another suggested the ECM may need replacement,
all of which are a few of the only origional parts that I have not yet replaced, my replaced parts are very long,

id like to start small, where would be te best ways to look for and how would I find a short, as for the other problems that were suggested, how do I check them out? Please keep in mind I lost my car diagrams, and cannot locate my volt/ ohm ect meter. I can normaly problem solve and fix this car as it is the second that I have owned of the same make model year and engine size, but honestly this issue has me stumped.

thanks, Dave