I'm a truck driver, with many years of CB experience, and I'm currently studying for my Ham licensing. I had already learned a lot about antennas over the years, but I'm learning more now with the studying. There are a few things I can say about your questions, and I am likely going to be working on this shortly myself, as my new-to-me Cherokee will be getting a CB some time this spring. I've been looking the Cherokee over for a bit now, and I think I may mount my antenna on the left front fender, opposite the AM/FM antenna on the right, using the same type of in-fender mount with a few mods to connect the CB antenna. Maybe. I did see a write-up on doing this on one of the Jeep forums. I'm not settled on the idea finally yet, but it looks like the best way to go I've seen so far. If I did do this, I could also modify the AM/FM side to use the same antenna (it'll work just fine for AM/FM), and have a visually matched setup for both sides, which would look decent. If I do it that way, I'll do a write-up with pictures and post it here.
Anyway, I run (in my big truck) a Galaxy 99 with a Messenger M4V, putting out about 900 watts, through 36' of low-loss coax, to a Predator 10k dual coil antenna. I do have an extra one of those antennas which would make for a killer setup on the Cherokee, but unfortunately it would also scream "steal me!" So I think I'll probably just run a 4' Francis if I run my old Galaxy 88 barefoot. If I decide to go with power, it'll be a headache, and that antenna would not be sufficient. My Messenger 450 would melt it! So I'll probably just run the 88 barefoot, or I also have a Connex 4600 that puts out 150 watts barefoot. The Francis could handle that okay. I'd rather use 5.5' on the length, as that would be more ideal, but it depends on whether I could get the Cherokee into the garage with that setup, especially after it's lifted. Aargh, there's always something, eh?
At any rate, what I can tell you is you want to avoid using a "no ground plane" type of antenna if at all possible, as they are inferior and quite problem-prone. Also avoid using a 3' if possible, as they will not get you any kind of decent performance. 5.5' is ideal, and the most I would compromise that would be using a 4'. Also, you want to avoid having to run a separate ground if possible, as the system will try to use the ground wire as the other half of a dipole, and can wreak havoc with trying to get any kind of good range or propagation pattern/shape. Best to try to mount the antenna in a way that the mount bracket is gounded. It will save a lot of headaches and give better results. As far as antenna height in relation to the body, if you use a coil-loading antenna, the coil must be above the body. But with a "stick' type antenna like a Firestick, or a Francis (which is better than a Firestick), you just need to have the top of it above the body, though the more the better. And use an 18' coax, no less, no more. It'll make setting your SWRs much easier. Also, no matter what anyone might tell you, magnetic mounts are a poor substitute for a good solid-mount. If you can find a good CB shop in your area, get one of their custom-made 18' coaxes. Try to avoid using the blister-packed junk you find hanging on the wall in truck stops, as it is just that, junk.
This is a lot of miscellaneous stuff, and every install is different, depending on a lot of variables. So this stuff is all just sort of general, but attention to small detail can make a huge difference.
Feel free to PM me with any questions. I'll be glad to help if I can. If not, I may be able to tell you where to look for the info you need.