IronClad, I'm going to be putting the same alt on my 88. I'm going to do a three wire setup vs the 1 wire though. Check out Mad enterprises tech article(s) on this. Maybe it will help figure this out?
Weird problem. I can see why you are ready to burn the truck down. Obviously no short or you would blow fuses or melt down wiring.
Your meter shows good battery voltage plus you said its new so it should load test good. Meter showing good charging voltage too. You said all connections are good.
Blower motors pull a pretty good load but regulator should sense it and alt output should cover it.
My first thought was the new alt pulley may be too big putting too much of a load on your eng but, you said same thing happens with stock alt and wiring. I think that new alt puts out 80 amps @ idle.
Is it possible your old setup was bad and couldn't keep up and now the new one is but, is too much of a load at idle? I don't know, just throwing ideas out there.
I'm not a big fan of one wire setups. Check out those tech articles and let us know if you figure it out.