Need advice for misfire issue

There are two good quality providers of complete wiring harness kits for CJs, Painless and Centech. I completely rewired a friend's '73 CJ with a Centech wiring kit and it was an awesome product. Each wire in the harnesses was even labeled individually for what it did.
Yeah.... I looked at those and actually called Centech. My CJ is a 82 with a 401 from a 71 Javelin in it (401-B4) and some other modifications. I'd be cutting up a "stock" harness to some respect anyway.

Making one from scratch using the pieced together one that was on it was a good "learning" experience. That's what I'm telling myself anyway.

in the process I'm putting a new custom dash (new metal cut to match new stuff) with modern instrumentation and a double din stereo system in it. LED's all around and a few other things as I go. In the past I'd sone some engine and drivetrain work on my jeeps over the years but had never tackled a big wiring job until now.
 
Just got my PCM back and plugged it back into the Jeep. I started the jeep and it was hesitant to start but still started. I have noticed that whenever I disconnect the battery my jeep will run fine for a little after I reconnect it. It will run fine for maybe a few days before the codes pop up again and it loses power. The first start of the day though it always kind of struggles.

Another thing which might be unrelated is often times when it struggles to start it blows the manifold vacuum line off at the elbow connection.
 
Guys. Sent my jeep to a technician and he said he has fixed it but I am hesitant on believing him. He tested the ohms from the coil rail connector to the pcm, and from the connector to the grounds and found no issues or shorts in the wiring. What he believes to be the issue, was a faulty connection. The thing is I would take the connector to the coil rail off and plug it back in all the time and the misfire would remain. Sometimes it would go away but it always came back. He says that he simply pulled the connection and cleaned it and replaced the faulty locking mechanism (red clip) on the connector. He said he did that and it ran like a champ for 6 miles. On top of this, he’s charging $480 for pretty much unplugging something and plugging it back in. I am worried that I’ll get the jeep back and the misfire will come back.
 
Guys. Sent my jeep to a technician and he said he has fixed it but I am hesitant on believing him. He tested the ohms from the coil rail connector to the pcm, and from the connector to the grounds and found no issues or shorts in the wiring. What he believes to be the issue, was a faulty connection. The thing is I would take the connector to the coil rail off and plug it back in all the time and the misfire would remain. Sometimes it would go away but it always came back. He says that he simply pulled the connection and cleaned it and replaced the faulty locking mechanism (red clip) on the connector. He said he did that and it ran like a champ for 6 miles. On top of this, he’s charging $480 for pretty much unplugging something and plugging it back in. I am worried that I’ll get the jeep back and the misfire will come back.
I mean charging you that much for cleaning the connector is kind of shitty, but it is possible that one of the pins was corroded or not making complete contact. I worked on a 2000 XJ that had corrosion where the wires went into the connector for the coil rail. It would run rough and stall occasionally, but it usually got bad enough where it would throw a check engine light. I ended up getting a good condition used connector and rewiring it and the issue went away.
 
He's not charging you for just fixing a little clip, he's charging you for the time to find the problem that was the little clip.

Now, if it's fixed, really, it's worth it.
 
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