Thanks to Andrew and Zak for their patience with lots of incredibly stupid questions, a mail provider with an allergy to binary files, and a user capable of screwing up the simplest of operations. That's customer service!
Had a baseline dyno run before the three stage manifold was installed and one after but as it turned out the tune upload was just the stage 2 file due to a miscommunication from said idiot user. The upload didn't go well and dropped into recovery mode. PM'ed Andrew while at the dyno, got a response almost immediately, called, got on the phone with Zak who walked me through the process to get back to normal operation. Did I mention the customer service?
The dyno runs which I picked up with the car the next day after the LSD had been installed showed the wrong tune was loaded (about 15-16hp increase, max) so another PM or three, an email with pics of the dyno plots, and Zak had the correct file emailed in minutes. But the car was already home so the tune was uploaded later that night.
The diff had to get past 500mi before we could run another dyno but it's got past the 1200mi break-in period now so it'll go in for fluid change and a dyno run this week if we can get our schedules to match up. I'll scan and post all three dyno runs as an update when the last one is available.
The LSD at 3.73 instead of the OEM 3.13 makes sixth the effective 1:1 gear and gets rid of that utterly useless overdrive, makes shifts easier, and the car quicker without sacrificing top end. So it's difficult to separate the effects of the manifold and tune from the LSD gearing. But I can say the drive home with the stage 2 tune and new LSD was boring and no different than before, at least it felt that way.
In contrast there was an unavoidably obvious difference after uploading the new three stage specific tune that night. Had to baby the diff for 300mi, take it easy for another 200mi, and keep my foot out of it and away from redline for the balance of the 1200mi break-in. Even so the car's a lot more fun to drive.
Up and down shifts are easier to rev match and smoother either because of the new final ratio or the improved low end torque or both, either way it's no longer the jerky pita BMW saddles us MT drivers with. I expect the CDV delete to make a difference only at the 1-2 and maybe a little bit at the 2-3 shift points where there's still a bit of annoying delay.
I'm not sure the final ratio change alone would be as good as it is without the improved engine performance, but together they feel freakin' perfect. It's the way the car should've been built to begin with imho. And the PE sounds seriously better than before, if that's possible.
There aren't any noticeable problems with power generation, no codes, no rough idle or hiccups, and we didn't clear adaptations either. For some reason mileage is about the same but of no concern, ymmv. Pretty impressive work, can't go wrong with AA and Andrew and Zak won't let you down, no doubt. (All work was done at Classic BMW, Plano, TX)