You cleaned all the wires to and from the altenator and battery? Checked your grounds? Battery posts and terminals? All cleaned.
As well you have no broken or burned or damaged wires?
Have you checked the output of the altenator yet? If still on the jeep the easy way is to start it and turn in all the high draw equipment that you can, ie rear defrost, high beams, heater fan on high, factory fog lights. Don't use aftermarket stuff, just oem jeep electrical, and see what the altenator is putting out at the battery. If its 13-14 volts ten its charging, if it's 12.
? Usually it's not but it should be over the rest voltage of the battery.
As well before starting the test, fully charge the battery, and see what the voltage is sitting at rest. The alt will always be over that, if less then you will have problems.
If the alt is pulled out already take it down to auto value, I think the do free testing of the alt on a bench.