What kind of budget do you have? I can't help a whole lot with the install as i have no clue what the inside of your jeep looks like. You want to make sure you can easily view it and mess with the controls while in the drivers seat... and have it in a place which doesn't require losing total sight of the road if you need to hit the hold button or change banks, readjust squelch etc etc
I personally own a 2051, a 2055, and a 2096. If you don't need digital then you can scratch the 2096. If you need digital then you can scratch the other 2. The only real benefit i've seen between the 2051 and 2055 is that the 2055 will do CTCSS/DPL... so if that is something you need then i would suggest the 2055. I don't have a pro-433 but i have heard good things. I believe the 433 comes with 20 banks instead of 10(still limited to 1000 channels though) i just don't know if it will do ctcss... also the 433 is rebanding capable.
For an antenna, i would personally go with a 5/8 wave VHF... it will do great on vhf, good on vhf-lo, and decent on UHF. Of course the 5/8 wave is about 49 inches tall so that may not be what you are looking for. If height is an issue then the maxscan1000 by maxrad might not be a bad choice. You will lose some lowband with the maxscan but gain much on UHF and 800mhz. I would(assuming you won't drill any holes) go with a gutter mount setup between your hood and fender. You could put a 5/8wave on the guttermount and it would still only be about 15-20 inches at most over the top of your rig. Also, if you offroad/backroad your jeep much i would definetely recommend an antenna with a spring unless you like replacing them every couple weeks.
There is nothing wrong with direct wiring or cigarette lighter wiring. I personally like to be able to run my scanner without the ignition on so make sure you have a power outlet that is "always on" and just hook your scanner into that. That also makes it easier to take out if you need to. I don't see anything wrong with portables other than they don't respond very well when attached to bigger external antennas. If you buy the handheld get a Diamond RH77ca(handheld) antenna for it and be done with it. Any antenna you mount outside your vehicle(in my experience) will only overload the handhelds and completely defeat the purpose of having that big antenna mounted on your rig.