UMCRubi, With a Rubicon's 4:1 and I am guessing here an automatic transmission?
Braking or even stopping is a problem. There are only two ways to do this, Increasing the hydraulic pressure the Master cylinder can supply to the calipers or increase the amount the pressure the calipers can use.
We will start with the second and most expensive. Big break kits require larger wheels for clearance for the bigger rotors, bigger calipers, and pads. So if your budget isn't ready for tires and rims...
Next is increasing the hydraulic pressure to the factory calipers. You factory braking relies on vacuum assist, a simple upgrade is a hydro assist unit that takes power from your power steering pump and uses it to help your braking. You can expect up to 4 times the braking power with this upgrade, but this is still a high dollar upgrade, some where around 1200$.
The first upgrade you should look at is Rotors and pads, some say ceramic others say Kelvar...everyone has their opinion here. I have a 01 with 4:1 and a automatic transmission, after converting to 4 wheel disc (factory drums on my dana 44) I still didn't have that crisp stopping power that I was looking for. So I have researched all the steps for my 01, the first was still a big hit but I went with EBC brake pads and rotors, the pads are better than anything I could find locally. They didn't fix the creep problem I have in 4 low but they made a big difference on the road. I still plan on doing the hydro boost, but at this time it can wait.
I hope this gives you some thought.