i had issues with destroying brakes in 40k when i was 16, but not now. you might want to try driving long and not accelerating when there is a red light in front of you, or if you already do that, then....
All Pro Offroad sells a rear disc brake conversion kit for a 3rd gen 4runner
I have the above kits installed on my 02 T4R and while the braking has improved, i no longer have an E-brake, and I have a 140$ FJ master cylinder, if you get the kit, try and get calipers that will work with your existing brake kit, or maybe you and I should get together and work on a transfer case parking brake for the 3rd gen. the kit is around 500 USD but so is replacing the rear drums when they go out, so thats why I did it, installing it by yourself is going to be difficult unless you have alot of tools, so try to have someone help you. good luck