All 'stage 2' from the suppliers I know are basic tunes, no hardware mods unless requested specifically, like EGR delete etc. Both Rocketchip and Malone are big in the VW TDI groups, I have tunes by both of these makers and will be getting another from one of them this summer for another TDI project.
Rocketchip is
here and Malone is
here. I've found Jeff at Rocketchip is better to call, he's almost non-responsive to emails. RC does publish their basic (stage 2) performance improvements on the website though, that's where I got the figures from.
Yes, I think Sixto is right, maybe Superturbodiesel is really what you're looking for?
I think many of the Benz diesel engines are used in a variety of platforms. The OM642 was available in the W211/W212/W221 cars while a variant was available in the 08 and up Sprinter vans. The OM647 from the E270 CDI was available in the early Sprinters in a variant that was very much liked by owners.
The same utuber i mentioned before has also done some basic trans valve body work to help the 722.6 with shifting etc. Otherwise I am not sure what can be done other than a professional rebuild that would include performance mods to support the greater torque of the tuned engine. That utuber also had a tune to improve the trans performance as well. He has a lot of vids, you won't have trouble finding his stuff. I think it's a popular channel and the topic seems to be popular.
Steve