There are many ways to fit 35" tires. The most common is a 1.25" body lift and 4" suspension lift. You can also use high line fenders, or metalcloak fenders and little to no lift.
Stock brakes suck with anything over a stock size tire. I don't even like them with 33's . A vanco big brake kit is one of the best investments you can make.
There are many ill informed people out there who think you need to trash the stock axles completely and swap in this, or that. 35's is the point you need to replace the rear d35c imo, but some choose to do a super 35 kit insted. They work well for many, but with my lead foot and v8 power it wasn't an option I cared to explore.
The dana 44 rear out of a tj, or lj will bolt right in , but the drive shaft may be to long since the dana 44 pinion sticks out further from the axle center line than the d35c.
The 95-01 ford explorer 8.8 rear is a very popular swap for the tj. It will need brackets welded on to bolt in, but many companies offer kits to do so. The 8.8 is cheap and they are abundant due to them being used in every 95-01 explorer. The dana 44 on the other hand was only an option in the tj and are hard to come by. The lj had a rear dana 44 as standard equipment, but the lj is a bit rarer in and of it's self.