joek3167,
There certainly is lots going on and I'm not convinced it's all related. I'm not an automotive electrical man so this is all supposition. You put system voltage to #4 and got the alternator to full field so I would take that out of your equation to start with.
The battery cable deal doesn't make sense. A clean, tight cable/post can take several hundered amps for 30 seconds and shouldn't burn your hand. Your system max's out a 54 amps.
Does your alternator connect at the horn relay? Is it functional? Those bulkhead connectors are pretty famous for getting fuzzy and screwing things up. You never mentioned if this truck has a idiot light.
I'm out of suggestions on this one. I will say that if I weren't concerned about stock appearance, I wouldn't hesitate to install a modern internally regulated alternator...10SI units are dirt cheap and you could even go the one wire route and maybe make it that much easier.
Before I did that, I would check and clean all the battery and ground connections as well as any bulkhead connections.
Do you have a wiring diagram for this truck. The few I have found show a 'GEN' light which is in parallel with a resistor coming off the back of the keyswitch. I'm not sure if a worn out keyswitch could cause havoc but I would take a look at that too.
I think all the regulators were the same units (non-transistorized) but were adjusted for the different output alternators on different vehicles. A 42 amp unit would work fine with a 54 amp alternator, it would just limit the alternator output to 42 amps. I would steer clear of the transistorized regulator for sure.
Good luck with this and be sure to post the outcome.
Stuart