The 4.0 with a 5 speed had some tranny problems,the trans is a Japanese unit also used in some Toyota trucks.The 5 speed was upgraded in the mid 90's I believe.Both the 86 and 89 5spd Cherokees I owned at weak syncros,specially 2 nd gear.The 96 we have now seems to shift smoother,I use Redline oil in the tranny,made a big improvement.
GMC Panel,does your Cherokee suffer from what I call hyper throttle response? The low first gear with the quick throttle and rubbery motor mounts makes first to second smooth shifting a little difficult.Other guys with stick Cherokees have told me the same thing.
I'm also thinking,like many late model injected engines,the 4.0 has a computer controlled rpm governor,around 5200 rpm.I don't see over reving taking out main bearings.
About the speed density injection on 4.0 Jeeps:a few years back I put on a free flow Dynomax exhaust,seemed to be a little slower after the change.A few days ago I replaced the rusted out Dynomax exhaust with run of the mill parts store muffler and pipes.The Jeep now is faster with better throttle response with the more restrictive exhaust.The stock SD engine management doesn't have the ability to richen the mixture to cope with a better exhaust and or air induction changes.
I don't know all that much about computer remapping,but it seems it will take a lot of on the road testing or dyno work to get it right.