My rig is trail only and I run the stock brake setup without any issues with the disks in the rear. Then again, I have an SJ-410. The lack of power anything to begin with probably means I can get away with more.

When converting to the disks in the rear we just put a T in the single line running back, split to the left and right calipers.
When doing 50 I can slam on the brakes and the rear will hop just a little bit on dry pavement, but I don't have the power to lock up all 4 tires with the 33x12.5 Pro Comps. I don't really see this as an issue, as I don't really need to go into a 4 wheel skid when doing 50 anyway.
SNJSamurai: I think that is similar to the guy in our club who put the line locks on his FJ, his had a remote switch available I believe, so he didn't have to run his brake lines through the cab. I have a drum brake on my transfer case, so I never had to worry about it.
