So many questions......
But here's a start. Since this is your first swap, I would suggest keeping it fairly simple, this way you are less likely to burn out and leave it unfinished and/or sell it at a loss.
That said, 1 yes, a 4l80e will bolt up to it since that's what it originally had. It would probably be best to find one that was originally bolted to an LS engine since there has been changes made in the wiring over the years.
2 Keep in mind that headers will probably interfere with your stock shift linkage. TBSS manifolds fit real well and on a stock engine flow good enough.
3 You can splice the PCM ends back on the harness, but it will be alot of work and leaves alot of places for simple mistakes to happen that can leave you pulling your hair out trying to track them down. For the cost of a truck harness, I would find a complete one and mod from there.
4 you can make your own adapter plates, all you are doing is making a way to bolt the original mounts to the engine. The original stands can be a problem with manifolds, so I would get a set of stands off of a 73-87 and use them with their matching mounts and clamshells.
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