Oh boy. You've stumbled into a hot topic. The long and short of it is this. The people that have done it are pros and won't release a free solution, the people that want to do it have little to no idea on how. You'd need to disassemble the code with IDA, or port the tuned file over to the stock manual binary. Which file is tuned? Tuned for what? Who did it? I'd be willing to help with what I can. Please upload the files directly here rather than linking, it makes things simpler.

Daz

If the ECU can't be coded to manual via VCDS, then the reason there is no "solution" posted is because this involves tons of work.
You can't just switch it over. I've done a few now, and getting it not to throw any code is the easy part. The hard part is stuff like recalibrating the whole idle control, dashpot, and so on.

Probably easier to take a manual ECU and tune it from scratch.

I realize that I am treading some hallowed ground asking such loaded questions. FWIW, I am a very resourceful/capable code smith. I am also aware that there have been many who have gone before me that have made a living from what I am asking. But the tinkerer in me wants to know how and why. That's all. Josh Alfonso will have my manual ECU on his bench tomorrow, he is the one who tuned the Tiptronic ECU for the PES G1 with FMIC, a setup that has long been out of production (c. 2001-2002, me thinks). The engine is revving freely and throwing no codes on the tune in the Tiptronic ECU until the car starts moving and then the speed sensors tell the ECU that the car is in gear and the alarms start blazing because the transmission is not sending data to let the ECU know it is alive.

I have compared the two files in a hex editor, and I agree, there is a great deal between them that is different, at least as far as was willing to advance into the comparison, line by line, which wasn't very far. I was discouraged by how dissimilar they were. the two ecus are for the same chassis, were manufactured 2 weeks apart, the only base difference being that the tuned one is for a Tiptronic, and the further differences may be attributed to the changes made by J. Fonz for the increased flow from the larger injectors, and increased air flow from the SC at the TB, plus whatever other voodoo is done on these units to make them purr.

I look at this as a hobby and now somewhat of an obsession because I know the answer is out there to be understood, I am just fishing for leads to get me tinkering in the right direction. Chances are that Josh will have a tuned version of my manual transmission ECU back to me before I will get my head around this, but I thought I would give it fresh go anyway. It is the puzzle sitting in front of me that is screaming at me to be solved.  

Please pardon the noobishness, but would I be on the right track for a starting block to use this .bin and apply it to the ECU file from my OE manual tranny 3B0 907 551 DB?

compare stock to tuned. find the differences. search your manual bin for the same maps, apply the differences. generally speaking of course. not everything can always be applied verbatim.
if you dont know how to compare hex then this probably isnt the project for you.

What you want to do doesn't require disassembly. First, you need to make an xdf. I outlined that process. Once you've done that, compare the stock file to the tuned file, take note of the maps that were changed and make the same changes to the manual ecu. By far the simplest way to do it.

Post up your xdf when you're done, there aren't any definition files available for 2.8 flashes.