robert, I've had the tune for approximately 4 years. I decided back then that I wanted to keep the WH for many years and and envisaged I would be putting at least 300000 k on it. It is a very capable tow vehicle, comfortable and it's offroad capabilities underestimated. I was aware of the swirl motor issue and my understanding is the EGR is not good for a diesel engine in the long term.
I wasn't happy with the turbo lag either, however I did eliminate this to some degree by putting a straight thru muffler and a high flow K & N filter. I added a Provent to reduce the sump gases/oil going though the engine and potentially gumming things up internally (nissans aand tojos are renown for this)
I also wanted a bit more power for towing my caravan, boat etc as the vehicle was purchased with this in mind.
I don't have any regrets in getting the tune, the power/acceleration of the vehicle when one opens the throttle is exhilarating, the vehicle pulls my 2.5 tonne van with ease and going up hills, does it easy.
Fuel consumption varies and depends a lot on the terrain, head winds, the load in the vehicle and what's in the roof rack which generally includes a kayak. That said it doesn't struggle at any time.I think I can safely say it's using on average 14l/100k
It's an enjoyable beast to drive and I probably use the throttle a bit too much. One thing I did do was add Murchison's 3"ss exhaust system, about 18 months ago,the difference was noticed according to the Scan Gauge the torque increased from 580's to 600 +, in hindsight I regret I didn't do that when I had the tune done.
The tune allows the checking of fault codes, you can take the tune back to the original tune if you want to and take it back again.
You mention the drive by wire being connected to the brake pedal, I don't believe the tune will eliminate that. I believe what you are referring to is drive by wire lag as opposed to turbo lag. Drive by wire lag relates to a delay when one pushes the throttle pedal and I understand that most modern vehicle suffer from this.
However this can be eliminated, iDrive, Plug and Go and RevHigh have throttle controllers that will eliminate this issue,
RevHigh make one specifically for Jeep:
http://www.revhigh.com.au/jeep-throttle-controller
Anyway, I hope this helps and I've answered your question.