Hi I'm new to this site, hopefully im doing the right posting thing.
I bought a 1994 Bonneville SSE and a couple weeks after I began driving it, it seemed to have a misfire. I changed plugs and wires, checked coil packs and ignition module. Now the thing is, it misses and jerks the car between 60-70, and around 100km/h. At a standstill I put it under a load and brought the idle up and down, and after about 15 seconds, all of a sudden it seems like something kicks in and starts to shake and chug the car. It never happens right after I start it but after a few seconds. Also the engine light is on but the scanner cannot communicate with the car. Any ideas anyone??

PCM may have gone bad

As you alluded to, the best way to start is to find out why the Service Engine Soon light is on. One obstacle you will run in to however, will be that of scanning the code, as you have already determined. In 1994, GM, in their infinite wisdom, used OBD 1.5. Essentially a OBD 1 computer, OBD 1 code set, with an OBD 2 plug. You need a scanner that can read OBD 1.5 codes. Your cheap scanners are going to be incapable of reading such, likely explaining the issue of the scanner not connecting.

Now, the PCM may very well be going bad, in all honesty that was not exactly a strong suit of the 94/95. I wouldn't call it dead just yet though, until you know what is going on with it.