There are two wiring harnesses out there, both of which are expensive for being a wiring harness, but since the can buss includes the radio, it's how things are now. One of them is for the regular sound system and the other is for the amplified 7 speaker infinity system. They cost $80-$125, but some people have found them cheaper on ebay. Since it's sort of part the computer system, I'd be leery of deals that seem too good to be true.
If you have the amplified Infinity system, but are going to bypass the amp, then the non-amplified harness is the one to get. It's what I went with.
Infinity 6020CS components fit nicely in the dash and the tweeters fit in the factory tweeter pods. Put the crossovers in the ends of the dash. They have excellent imaging and bright highs without being harsh. Infinity 6022SI coaxials are a nice complement to those as they have similar efficiency, power handling, and frequency characteristics while being shallow enough for the sound bar. The impedence for both of these speaker sets is 2 ohms, so that's another reason why they work well together, especially with a four channel amp as the F250 in my signature pushing them.
Next up is the sub. Cheap plastic is a poor choice of sub-enclosure material especially in higher powered systems, so changing out the factory sub and keeping the enclosure isn't really the best way to go. To have bass, you have to move air. This is why I have never been impressed with shallow mount subs. At first, I got a 10" Infinity Perfect sub, but returned it because it just didn't have the oomph I needed. I then got the 10" JBL P1024. It's a dual voice coil sub, is very deep, and has a very sturdy frame. I wired the dual voice coils so it presents a 2 ohm load to my amp. I'm pushing 600 watts continuous to my sub. The key to the exceptional sound of my system is balance. The bass is tight and controlled, hits hard, and really sounds like drums but does not drown out the highs or muddy the mids. The thing that impresses people that have heard my setup is it sounds great with ANY music. Heavy metal, classical, jazz, rock & roll, rap, country, blues, whatever, it sounds fantastic with great imaging and stereo separation. You can turn it up really loud and it never distorts or becomes harsh. I have the optional blue tooth modules for my Alpine head unit with the mic mounted on the left side of the windshield, tucked into the plastic trim. Call quality is great and it pairs with my V3XXX RAZR nicely. It allows me to dial numbers in my phone's phone book through the head unit and the caller id displays on the screen. I went with a cube shaped sub enclosure that has an angle on the face that matches the angle of the back seat. It has quick connectors on the back of it, so if I need extra cargo room, I can easily remove it. With it in place, even though the enclosure is bigger than the factory one, it takes up less room because it's in a better location, against the back seat on the driver's side.
It's not a competition system, but I believe the only way to get better sound is to spend substantially more money and convert the whole rear section of the Jeep to a large array of subwoofers, amps, etc.
I took the lady that sold me my Jeep for a ride and let her listen to my sound system and she couldn't believe it and started singing along. She was also very pretty, but married unfortunately. My signature has all the stuff I did listed.
My sub and head unit came from crutchfield. my amps and speakers came from hooked on tronics. My sub enclosure came from a local audio shop.