It sees that conventional wisdom is to not go any bigger than 33s on the D35 diff that is in the rear of most YJs and TJs, especially if you plan on any serious offroading. Apparently, the D35 is a weak link in an otherwise good drivetrain. There are a lot of upgarde options, the two most common being the D44 from a Cherokee and the 8.8 from the Ford Exploder.
A lot of rigs run the 4" spring lift and 33s with no further mods, so that may be the way to get started. If you have the means, there are certainly many other options and upgrades, and depending on what you want to spend, you can get pretty crazy.