Can't figure it out

Ok are you ready sir haha bc here we go. I am going to explain as best as I can to paint as clear a picture as possible on trying to find the issue I am having. This is over the coarse of about 5 months with several mechanics not being able to figure out the problem. This is explained to the absolute best as I can. I have a 2003 chevy s10 zr2 with a 4.3 liter 6 cylinder engine. Back in October of 2015, I blew a head gasket and ripped out 3rd and 4th gear in my tranny. I then got both the engine and tranny replaced and the engine that was put in was also a vortec 4.3 v6, but it was off of a 2002 s10 with approx 150,000 on it. My original was a 2003. After getting the truck back everything was running as it should other than 1 problem. While on highway ONLY, at approx 70-75mph, my check engine light would begin to FLASH and the truck sounded like it would bog down or that it was missing on a certain cylinder. So we did a OBD 2 test which revealed p0302 (cylinder 2 misfire). Replaced spark plug, which did not help the issue. So my mechanic said it may still have been loose or damaged vacuum lines. He also did do a compression test on that cylinder which came back good. This went on for approx a month but I did not drive the truck that much. So we then decided to move forward and so I took it to another shop where more tests were done and they concluded that I needed a new distributor and MAF sensor. So I got a new distributor, cap, and rotor, and sensor. Installed them along with another new spark plug in cylinder # 2, but had many issues getting the timing correct and so therefore I could not get the truck to start. (I NOTICED THE SPARK PLUG I PULLED OUT SMELLED VERY STRONGLY LIKE GASOLINE) Had it towed back to shop where they re timed the engine to TDC and got it running again. Picked up the truck and drove it home on highway and sure enough, engine light still flashing at 75 mph and still misfire type conditions. Ok so got home and put code reader to it, still reads p0302. Inspected vacuum lines and did find that one of the vacuum lines was not connected properly. (On this truck, there is a line that comes from engine all the way over to the driver side front fender where there is a small nipple that connects the 2 ends of the vacuum line). That vacuum line was not connected, so the connection was made. Ill be damned, truck runs great. No flashing and shifting is good like everything should be. Drove around the next day, no issues. The next day, I decide to take the truck to a family farm to pick up four wheeler and while about 25 miles down the road traveling at highway speeds, same problem comes back. Flashing engine light and misfire conditions. I drove approx 10 more miles like this and decided to get off highway. Once I got off at nearest exit and started coming to a stop, the truck really bogged down and died. Attempted to restart and truck would start but just barely stay running until it would die again. At this point the only way to drive was to use 2 pedal method. One foot on gas while other on brake. So here I am stuck with only a few tools with me. The way it was acting and sounding, I thought the cat converter went bad and clogged up. I remember this bc this happened 2 years ago and I had cat converter replaced then. So with no options I removed my O2 sensors in order to see if maybe the cat was bad by releasing and gases or pressure that could be backing up. I did not have the special O2 sensor removal socket so I unfortunately cut the wires in order to get wrench on to remove sensors. Now of coarse the truck runs like shit and still wont idle bc of O2 sensors. Once again had truck towed back to original shop. Bought all 3 brand new O2 sensors and intalled them. Truck started up and idled for a few minutes with no codes coming up, but the cat converter got too hot too fast. Bad Cat? Mechanic removed exhaust system and completely gutted the entire cat and reinstalled system. He also inspected and found 2 additional damaged vacuum lines. So he then repaired all vacuum lines, however no vacuum test was ever performed on this truck. Now the truck is again not starting or if it does has very poor idle. The best way to describe what its doing is it will crank and wants to start up, but the engine seems like its jumping or misfiring completely. Almost like its being choked if that makes any sense? Did some research and mechanic though possibly a bad ignition coil and ignition module. Had both of those replaced and still no change with truck. He then thought bad computer. Had a new computer handy so he plugged and played with the new computer and nothing changed. WTF! Did more research and possibly found the answer. New crankshaft position sensor? Bought new sensor and went ahead and got new plugs and wires. Come to find out that when he installed the different engine, he did not do a relearn procedure on this newer engine like he was supposed to. So today, installed new sensor and that again STILL did not do anything. Now truck is throwing p0300 (random misfire) and P0101 (MAF out of range). But the MAF is new. I cant perform a relearn procedure if the engine will not idle right. So at this point me and my mechanic are completely lost for ideas. We cannot figure this damn thing out? Is perhaps the timing on the crankshaft off again? Or what about fuel? Possibly spider fuel injectors are bad? I already replaced fuel filter about a year ago. Just a thought but I do have an aftermarket Spectre air intake system installed as my air filter and ironically after that install is when all the problems began. I am going to replace all the spark plugs and wires asap and see if that does anything but with my luck thats still not the issue. If there is any advice you have or anything that you can think of on what could be the problem and what steps to take next. Sorry this was long but I had to make this as detailed as possible for you. Thank you so much for ANY input that you may have.

New parts replaced:
Engine, transmission, MAF sensor, O2 sensors X 3, vacuum lines inspected, ignition coil and module, gutted cat converter, inspection of computer, crankshaft position sensor. Wires and plugs to be replaced next.