Bob, I just realized your previous post said fuel delivery was set to 90cc. That is HUGE, should be enough to support nearly 300hp, and it's why you are seeing so much black smoke. Definitely turn it down if possible. For reference, a 6mm element pump maxes out at less than 80cc; and a stock OM603 six-cyl pump is ~52cc.

The transmission is a separate topic. A "shot" transmission will either not shift or go into gear, or slips / flares badly, and I haven't heard you mention any of those maladies. You are correct, the vacuum modulator controls shift firmness. With no vacuum it would shift firm all the time, which isn't pleasant at light throttle. Has a known-good vacuum modulator been installed and adjusted? Also, remember that the diesel vacuum modulator receives a vac signal entirely based on throttle position, more on this below.

Shift timing (rpm) is entirely based on throttle position, via the Bowden / control pressure cable. If the injection pump is pushing too little fuel (bad ALDA, stock pump out of adjustment, etc) this can result in late upshifts. The late upshifts will also be too firm because your foot is further into the throttle, reducing vacuum, making the shifts firm. The opposite is also true, with lots more fuel you aren't moving the throttle as much, so you would normally end up with early, soft shifts; maybe evening slipping/flaring if the vacuum level is high. I don't know what Dieselmeken recommends to get the transmission shifting appropriately.

Once your power gains become significant - basically once you get a larger turbo - the stock 722.4 transmission will be inadequate for the amount of torque produced. At that point you'll need to upgrade to a 722.3 which if built propery, can handle anything the 602 can put out with your Uberpump. The "custom" part likely just means an extra clutch pack internally (used on 6L M119 and M120 engins making 400hp with the 722.3) and possibly some fancy aftermarket friction discs. Nothing special should be needed. The donor trans will probably need to have a diesel valvebody in order to shift properly, I don't think a gas tranny will work without a lot of effort (if at all). If your mechanic hasn't done this stuff before, find a place that knows what they are doing! The driveshafts may also need to be replaced due to different lenghts.

BTW, what kind of EGT's are you seeing now, assuming you have an EGT gauge? It's possible that with a turbo upgrade and sensible fuel delivery settings you could avoid an intercooler for now, but an IC will be needed if you want to really turn the power up. Check out the liquid-to-air IC used on this S124 wagon build with a 606. Posts 7, 30, and 33 show a good amount of the plumbing:
https://www.*********.com/forums/showthread.php?t=11236

Edit: Replace the asterisks above with "500E board", with no space in between. Apparently, PeachParts has a problem with 500E's. Lame.