Well, you asked two questions here that could be several pages of posts in themselves.
On the transmission front:
A wide ratio CJ T-18 is the ideal swap as it will bolt in and have the correct adapters. However, these are not real common and are highly sot after so they tend to be relatively expensive. There are other transmissions that will get you lower gears but will require extra parts as in a wide ratio scout T-18, which has other issues, or aftermarket adapters as in the Ford T-18 or NP435, GM SM465 or SM420. I would recomend you do some research into all of the above.
Novak Jeep Conversions - Home is a good source of information on all of these. In any case you will need to get the drive lines lengthened on the front and shorten on the rear.
On the roll cage:
I would recommend a roll cage, but there are many details to consider. The first one is are you a good welder or know a friend who is. This will limit or open your options. There are many details of cage building. I can not help on sources as I plan to build my own. If you need a bolt in type cage then that is way different then to plan to buy a kit to weld in. Also you need to consider the type of wheeling and terrain you will be wheeling on. A cage that may do fine for rolling over once in a short steep area will likely come apart in a high speed racing crash or in multiple rolls down a long hill. However, a cage only needing to take one roll will be easier to make an not need as many members intruding into driver and storage space. You also need to consider how and if the cage will be tied to the frame, and how the seats and restraints will be attached. There are 2 schools of thought, and one common school of non-thought on this.
One is to tie the cage to the frame such that if the rig rolls it all stays togeather. Personally I like this idea. It prevents legs from possibly being trapped under the dash and allows the cage to be used to roll the Jeep up right after a roll over. The down side is that the frame tie ins can be a lot of work and often lead to the body being more tightly tied to the frame leading to more vibration when driving.
The second idea is to tie the seats and all restraint points to the cage but not tie the cage to the frame. In theory at least such a setup will lead to the cage posibly separating from the Jeep but keeping the driver safe in teh cage. However, the cage should not be used as a pull point as it is only tied to the body.
The last school of none-thought as I have called it is sadly the most common. It involves building a cage that maybe hell for stout in itself but will no thought to how it will stay or will of part from the frame and body. Often such setups involve the seats bolted to the body, the cage bolted to the body and the seat belts or other restraints bolted half to the body and half to the cage. Often not thought is given to how the cage will preform if it comes off the body part way or all together. Granted many such cages seem to do okay as most rolls are low speed rolls onto the side and even the stock roll bar often does okay in such cases. However, a cage makes people feel safer and take risks they other wise may not so it is best to think a cage design all the way through.
77 CJ5 Renegade w/304 and 3 spd. 
Linear Mode
