When me and Lee worked on that engine we tried to re do as much of those RTV disasters as possible, the ones we didn't get to were the things on the rear of the engine. I'm glad you guys are getting those taken care of.
As for the spark plug hole i can't remember if when me and Pat did the plugs and wires if there was a bad plug boot. The plugs are Denso Iridiums and are pretty new, i would try to keep them safe to be reused ($13 each) but maybe that hole needs cleaned out and new wires installed just to be safe. If the corroded hole is on the coil side you'll need new coil boots, I don't thing we replaced those and if the boot cracks the truck will run like [censored].