Mikeyd, the 3-4 shift flare is not necessarily a trans defect, but more likely a symptom that things are getting sloppy in your clutch stacks. They're set up a bit sloppy in the first place but the MB controller adapts shifts to the clutch wear by delaying shifts and modulating engine power, albeit quite imperceptibly. Ole's controller does not have this feature so you get what's really there.
If you are opening the trans up and swapping clutches, a lot can be done. Mainly, you can tighten the tolerances (some say as much as 50%!) of your stacks and remove spacers so you can add clutches. This may require ordering different spacers and/or snap rings for each stack. This is what I'm dragging my feet on at the moment. Not a big deal, just hate going to the dealer. You shouldn't have to touch the valve body with the engine you're using. If 800 hp maybe.
There are updates to some valve body pistons on earlier models but I wouldn't worry unless you're above 200K on the unit.
Yeah, I'm looking forward to low revs and better mileage too. Keep us posted!