Low end torque is much better than stock. The one I have moved everything back and tucks up and in tight. The skid plate covers the cross over now and I can now lift it higher than 2.5 without having to deal with the exhaust again. Mine is just a little louder than stock and I didn't notice a drone at freeway speeds.
Not sure what caused your problems and probably never will since I'm not setup for crawling.
You dyoned it? I doubt you got 5 rwhp at redline let alone anything at the low end.
Personally, I find (and like) that a freer flowing exhaust and intake will make the engine feel more responsive especially if you have a manual transmission. I have them and do not regret these modifications FWIW. Just no HP unless you get a tuner and higher octane fuel.
If you want to make power then you need to get a tuner that will advance your ignition timing and require you to run 91 octane or higher gas. Do this on top of the intake and exhaust and you will be making some HP that should be reflected on a dyno.
Anyway, the stock exhaust is already stainless steal and already has mandrel bends except for that flat spot near the curve by the rear axle. The pre-silencer is also straight through just like the pre silencer in the Borla.
The front section of the stock exhaust is already pretty well tucked up into the frame so IMHO the argument that the new exhaust provides more clearance is almost moot.
The only restrictive part of the stock exhaust is the muffler itself and even that is questionable. Granted, it is not a straight through design and you will feel a difference in responsiveness once removed.
The Borla muffler on the system that has a pre-silencer still hangs down nearly as low as the stock muffler.
On both the two silencer models as well as Borla's "rock crawler" exhaust which is straight back and has just one can, they make the shiny chrome tips stick out prominently from under the rear bumper. I kept smacking mine up in the trail - more so than the stock exhaust.
Me, I am a crawler so need all the space and clearance that I can get and have already ruined a couple of exhaust systems, the Borla being the easiest to destroy because of how low the muffler and tailpipe hang.
The exhaust that I run is the Flowmaster HP2 and that one does tuck up slightly more than the stock exhaust and others. The tail pipe is also pretty well tucked up under and it took a lot of effort before I finally knocked the tailpipe slightly out of round on the Rubicon - but not oval or smashed flat like you see on a lot of other jeeps that heave seen some trail time.
Muffler makes next to no difference. Placebo.