I am also having trouble with the blower motor on my 2000 TJ. I have tested the motor itself by hot wiring it to the battery and it turned. I have two 2000 TJ's so I've been able to swap parts without buying anything yet.
I have tested the relay, resistor, motor, and both switches and all seem to be working fine on the "other" TJ.
The only thing I've noticed is that when turning the ignition switch, I cannot feel a "click" from the heater relay as you normally would. Which indicates to me that no power is coming into the relay.
Any thoughts would be appreciated.