OK so after much research I found that the only style of these radios that will work in a TJ (due to the CANBUS system) is this one particular model with the code of RAQ. If my picture was more clear you could see to the left of the tuner knob and to the bottom right of the AM/FM button is where you will find this code. This is the very informitaive source I used in helping me figure all this out The Chrysler-Huntsville RAQ CD Stereo Head Unit: Repair Guide
the wiring harness I ordered and used was this "old to new style factory radio stereo install wire harness adapter #82207541" link for ebay: Old to New Style Factory Radio Stereo Install Wire Harness Adapter 82207541 | eBay
The harness does come in two sepersate pieces and you will need to wire them together. You will notice that the connector that goes into the RAQ radio has two(2) yellow wires as well as two (2) black wires. Both of the yellow wires connect to the one yellow wire on the TJ style connector, and both of the black wires need to be hooked to a ground. I found a brown wire in the RAQ side harness that did not connect anywhere on the TJ side so I just taped it up. Simply match the rest of the colors and connect by which ever means you feel is most suitable (solder, butt connectors, wire to wire etc.).
The radio is a very tight fit into the hole on the TJ. I did not take pics but suppose I could if it would help someone but this is what I did: On the bottom of the radio (left and right sides) there are two bolt holes that I used a dremel to cut off, just simply cut the square off where the bolt hole is, it is all plastic and will not damage the radio in anyway, there are also two aligning pegs that also need to be cut off. I don't remember the exact location of them but they are pretty obvious and need to be cut off as well. Secondly on the inside of the TJ radio opening you will notice that on the top and bottom in all four corners there is a raised portion of the plastic. I simply used my dremel with a grinding/cutoff wheel and ground those areas down flat. I plugged in the harness to the vehicle side, plugged in the antenna to the vehicle side, then hooked both to the radio. Even with the key in the off position you will hear the CD changer start cycling. I let it go through it's complete cycle before turning it on for the first time. After it was done, i powered it up and everything worked wonderfully.
This particular stereo will let you eject cd's even with the ignition in the off position. You can not load them though only eject them. I am on a 24 hour duty shift today so I will not have the chance to work on the bezel but that is the plan for tomorrow. I will likely run to the junkyard tomorrow and grab the center bezel from an 06 TJ and hack that one up so that I can also get the added 12volt power source, as the newer ones have two instead of one. It will also give me the option for four rocker switches instead of the three spots I have now (not that I am even using the other two I have now), it's just nice to have the option.
Any questions or advice thus far feel free to chime in or ask.