I don't have the time currently to give you as much detail as I would like, but I think this may be helpfull.
Here are a few critical things that you will want ASAP, in some sort of priority list.
1. Front and rear tow points. Could be bumpers, stock front hooks (junkyards) with brackets, rear tow receiver (Junkyards), etc.
2. Rocker protection (AJ's comes to mind)
3. Front and rear diff guards (TONS of options here, any of the

vendors to search).
4. Stock gas tank skid (search junkyards).
5. Transfer case skid (look at DPG off road).
6. Tools, hi-lift, first aid kit, etc.
Lift kits, Stick to Rubicon Express, Old Man Emu, BDS, Rusty's, Clayton, DPG. You can search all of them for different sizes, search on Naxja, etc. But stick with these basic companies and you should be OK. Rusty's will be on the cheaper end and OME will be on the upper end.
The difference in cost between a 3" lift and a 4.5" lift is the following (read this as "understand these items").
1. SYE (Slip Yoke Eliminator), and new rear driveline.
2. larger tires (32's or 33's? instead of 31's)
3. Gears (you will NEED gears for larger tires, not as necessary for the 31's).
4. IF you are doing gears, set up is cheaper to add locker or limited slips at the same time (this is an EXPENSIVE proposition).
I hope this starts to help.
Michael