1998 Plymouth Voyager Rough idle/stalling/check engine ligh

My van sat for one month before we put a new transmission in it. Two days after it was on the road the check engine light came on. Took it to Autozone and the diagnostics said the engine was misfiring randomly. Cylinder 2 and 6. Replaced plugs and wires and had code reset. A couple of days later light came on again went back to Autozone and it read random misfire. This time it was cylinders 2 and 4. I replaced ignition coil because the resistance was a little funky. Light still came back on. Took it to a shop and paid $105 for them to run a detailed diagnostics on it. They told me my engine is randomly misfiring and that cylinder 2 was not firing properly. Duh! They said I should replace plugs and wires and would not listen to the fact that I had just done that the week before. So this is what it is doing. When I am driving at speeds above 45 or 50 the check engine will start blinking. I researched this and found out this is actually when the engine is misfiring. It never does it at low speeds. Also you can start it up first thing in the morning and it runs fine. Sometimes and not always if you turn the car off and then restart it it runs really really rough. Then you put it in reverse and it shakes really bad as you back up. If you can drive without having to stop it will usually work itself out, but if you get stuck at a stoplight the van will usually stall. Then when you turn the key it will just keep turning but will not start. You can either push on the gas and it will start after a few seconds or you can turn the key off and then try to start it again and it usually catches and then it runs just fine again. It seems to be doing it more now that the weather is getting warmer and the engine does not have as much time to cool off. I have also replaced the PCV valve, sorry just remembered that. Any suggestions? I just don't have the money to take it to the dealer for $105 an hour for them to dig around until they figure it out. Thanks!