What can still cause misfire codes after all this work? Misfire on cylinder 5 and 6

Thank you Roy (ASEMaster6371)for your input. I would get an opinion from another shop, but nobody around here is willing to give their direct opinion. They give me a run around answer that does not help me. I even went to an auto electric shop that totally danced around the question by giving me examples of issues that have come in to his shop, things that happened to that vehicle while in his care and that he wasn't responsible for. So he was definitely not going to throw anyone under the bus. Nice man, but did not really want to help me pin point a cause or that it could have in fact been due to the repairs from the shop. As far as the shop who did the work, I really don't care to return to that shop for anything after what happened. I don't trust my vehicle to their care any longer. And to explain further, the codes that were there when I took the truck in were misfire on cylinder 5 and 6. Only after they did their repair work, did all these other codes come up. Now, the thing I don't know is, if these codes were there before or after the alternator was replaced, but when they called and told me I had to go to a Dodge Dealership for a PCM, and I picked the truck up and drove it there, those were the codes they put on their receipt to me. After the new PCM was installed, those codes went away. So I guess I will never know if it could have been a loose connection somewhere and I really didn't need a new PCM. The Dodge Dealership act like they looked over some things first before deciding yes, you need a new PCM. My biggest mistake in all this was not asking for my old parts. I usually do that, but I was just so upset I had to spend another $1050 on my truck when it initially went in for a tune-up, I wasn't thinking at my best. I did call a few days later, and of course and conveniently, all the old parts were gone, or turned in for the core, or whatever. So I'm screwed any way you look at it.
Now that I have the truck back and have driven it a few hundred miles, all the work and testing that was done on it, the misfire code popped up again after I filled the truck up with gas. This truck has had that code pop up intermittently for several years and eventually it would shut itself off or I would take it in to shop and have them check it and shut it off and it would stay off for a long time. It has always passed emissions. Before now it was usually just misfire on cylinder 5. Now it added 6. That particular shop did a tune up and then checked it again and it still had the misfire codes. I asked them to do a compression check. The compression check showed PSI's from 155 - 170 with 125 and 135 on cylinder 6 and 5, respectively. Although I did not ask or authorize them to do anything else, they then did a leakdown test and both cylinders held at 75PSI (which I am not sure what that indicates). They then did a smoke test for vacuum leaks and it had no external leaks. They then checked the injectors and they were ok, so they removed injector 5 and replaced it with the injector from cylinder 1 and still cylinder 5 had the misfire. They did a recheck for firing order and spark and it was ok. They removed the crank sensor and it tested ok. They checked the injector with a noid light and it had pulsation. They kind of indicated to me that they weren't sure what the problem might be after all this was done if it still had misfire codes after the new PCM. I know the compression in 5 and 6 is low comparatively speaking, but would that cause the check engine light to come on. And also, after all this was done, plus spark plugs, wires, rotor, cap, valve cover gaskets, thermostat gasket, is anyone still positive they could not have caused the PCM to go out. That is a lot of testing around a lot of wired areas without disconnecting a battery cable. I know some of this stuff cannot be done if a cable is disconnected, but a lot of it can be done with a battery cable disconnected. The Dodge dealership disconnected the battery cable just to replace the gasket between the air cleaner and the throttle body. I only know this because I had to reset all my radio/clock settings.
Anybody can email me direct at shunt0202@msn. Com and thank you all for your input. It's all been very helpful to me to try and understand all this. I am not a stupid person and I used to even help my brother in law work on cars (with carburetors, points, etc) but all this computerized stuff on vehicles anymore gets a bit confusing and I am a very computer literate person (PC's and laptops)
Anybody can respond to me directly at my personal email shunt0202@msn. Com if you prefer that method of communication. And thanks again to anyone who has responded to my questions. It seems that the more information I am fed, the more questions I have.