your air cleaner might be partially blocked? Mine used to get water on it which would soak into the paper element and it would do exactly that, get wet and block up.
With a blocked air cleaner element the engine can't burn all the fuel (black smoke, and sometimes lots of it) and lack power.
This could also cause a build up of soot on the exhaust side of the turbo reducing turbo efficiency to the point that it won't work at all and will require taking apart and cleaning with toluene (on the exhaust side, not the side thats easy to get to).
Also the induction pipes (between charger and turbo, and from turbo to aftercooler) may be leaking causing loss of boost. This would be the easiest to fix, I took my charger and all the pipework off and pot a volvo "sports" filter on the suction side of the turbo, it's a round filter, not a flat rectangle one, I sealed the pipe from the turbo to the aftercooler with loctite high temp liquid gasket and put some insertion rubber under the turbo clamps. This sealed everything up, and I only miss the supercharger, um... I don't! The unrestricted turbo boosts up at about 1500-1800rpm, there's less load on the motor not turning a supercharger and i had no crossover problems, indeed I had less problems altogether and more room in the engine bay to work on other things.
I've been running this engine like this 14 hours a day, 200 days a year for the last 6 years without too much drama, it's actually a 42b and it's in a 9.9m alloy cruiser, commercial crab boat.
A previous boat had a 42a and (while I was a decky on this one) it did the same thing, blocked filter causing a clagged up turbo which supercharger or not is a restriction causing smoke and loss of power.
Bypass your supercharger and try it.
