Low charge when hot.

LivewireBlanco said
The only thing not stock is it has a relay that accounts for the crappy bulkhead connector and a bypass wire from alternator to the starter relay to help charging. Everything works great when it's nice and cool, only when it's hot does it barely charge.

LivewireBlanco said
charges great

We commonly say charges when discussing alternator producing power.
If that's what you are infering from the voltage readings, that's fine.
Just be aware that the battery may not be charging even when voltage is above 12.8
Without an ammeter, we generally assume it is, and that's fine.
When troubleshooting a problem like this, there is a possibility may not be charging the battery regardless of voltage on a dash meter.