Assure your wife you made a wise decision and a necessary one.
I did not have a transmission failure but surely would have had I not recognized problems with it. I had a trans replaced under warranty then had it upgraded with an aftermarket valve body, shift lever, heavier front band strut, billet accumulator, and a new set of clutches when I started to notice some of the same issues coming back.
First trans, missing spring on accumulator. Result, smoked clutches and burnt steel bands. All kinds of debris in trans. Symptoms, delayed (hang) on 2-3 upshift. Would not chirp 1-2 anymore. Why, slipping. Clutches and steels were repaired but the valve body that was put in as a replacement was a piece of pooh. Tech condemned the trans b/c he was fearful it had suffered other damage from all the debris. I feel the valve body was the culprit but was not going to argue with a new trans instead.
Second trans. Started to notice hang on 2-3 again. Decided to contact HTS Transmissions and got above parts. Dealer agreed to install the parts and with 4K on new trans front clutches were smoked already when it was pulled apart. Why? Valve body pressure issues cause timing problems on shifts. Upgraded valve body with higher line pressure (plus other parts) helps keep trans from slipping on shifts. A shift at around 6K with over 500 ft/lbs of torque does not do good things to clutches when it slides into gear. This is pretty much the case with the factory valve body.
My opinion on the torque management that is part of the factory tune is that it is an attempt to mask this problem with the 48RE. By cutting timing they were attempting to minimize the torque being applied to the trans under WOT. Putting tunes in that removed the torque management just made the failures happen sooner. I feel it would have happen regardless on most transmissions. I am sure some got lucky and got a good valve body but most did not, hence the problems we see in the autos.
This was my experience and opinions with the trans. I am very pleased with how it shifts now with the new parts. The shifts are hard and fast. Just hope it lasts. Only time will tell.
Hope this helps...