HEI Conversion Question and Holley 2280 Lingering Issue

The first red flag I see is why the HEI? Did it originally have lean burn?
2nd red flag was when you were talking about the overcharging and the added relay. I've never had to add a relay to make the charging system behave.
I have an 85 version of your truck, biggest difference is mine has a /6. I too had to go thru the wiring and added a fuse box under the hood thereby doing away with the fusible links. I went to a junkyard and got another harness as mine was just so damn butchered by past year ownership, best place for that original harness was in the garbage can. It was beyond repair, actually it had been "repaired" haphazardly many times before I got it.