Harley charging system question- I have a late 1984 HD Softail the voltage regulator seems to be getting warm & will this effect charging?

Its a shunt regulator which means it "shunts" or grounds to turn off. These type of regulators will always get hot as they have to absorb the extra voltage which turns to heat.they are cheap but the downside is that the stator is always outputting voltage even when it does not need to. It will work just fine when hot but many people myself included will replace them with solid state regulators that actually turn off. Cycle electric makes great solid state units for Harley. look them up, do some research and decide for yourself if you will benefit from one

Voltage regulators get warm! That's why they have a heat sink on them.