Ford Truck Enthusiasts Forums - New engine in my 92 running rough

I am normally on some of the other forums but need some help with my 92 f150 super cab 4x4 302 auto. I bought the truck new. At about 135000 my brother blew the oil pan gasket pulling a trailer. It had never given any trouble up till then. There were several cylinders with low compression so I had a rebuilt engine installed. It never seemed to run like before and about 5000 miles later the tranny crapped out so I had it rebuilt. Now I have $5000 in a $2000 truck. When the engine was installed they put on new repo exhaust manifolds. They seem heavier than the originals. I have had a terrible time with plug wires I have been through half a dozen sets.They seem to get hot and start shorting out. I have had it back to the shop that installed the motor 3 or 4 times the local Ford dealer and a second shop. Each time it runs well for a little while then starts missing at about 35 to 40 mph. When you look under the hood in the dark you can see sparks from the plug wires in many places and around the coil. Like I said I have tried several wire sets mostly NAPA, plugs, catalytic converter, erg valve, etc. I put a new alternator on and that seemed to help for a while. Before the alt. the check engine light came on after you drove about a half mile now it takes a couple miles for it to come on.You can’t hook up a code reader to a 92 as I understand it and the shops seem to have a hard time setting the timing. Sorry this is a long post but I appreciate any help you guys can give me.

Thanks stubbfarmer