The 2000 harness is pretty easy to install, but there is one mistake in the directions regarding the backlighting wire (orange) use to light up the HBL and wiper switch.
The directions tell you to connect it to the 5 position connector, to the TAN wire (on the a/c heat controls). It should go the orange wire! If you connect it to the TAN wire, you just connected it to your blower motor.
I do not think this is what you did, but rather check to make sure you plugged the correct wires in the correct plugs (cluster, etc).
Also, take a look at this link to see if you wired your 10 pin plug correctly:
Hardtop wiring: converting plugs to match different years - JeepForum.com
Does it blow fuses WITHOUT the 10 pin connector plugged into the hard top?
Also, DO NOT CONNECT THE PINK/WHITE and YELLOW wires at either end, you will not use them as the 2006 hard top does not have a dome light (as 06GoldenEagle stated).