I also have a 87 300D. Not quite as good of compression as yours.
I've done lots of things to mine to get it to run better. It is night and day different from when I started. But it was really slow when I acquired it 6 years ago. It now runs like a stock V-6 gas motor, but it has more torque than upper end horsepower. It runs out of steam around 3600 rpm.
Installed Monark injector nozzles and set the pop off pressures.
Advanced the timing a few degrees over factory.
Adjusted the ALDA / disabled it-this was one of the most noticeable increases.
Disabled the EGR and cleaned the crossover pipe and entire interior of the intake manifold.
Upped the boost to 14 psi from 11. (not that noticeable of a difference, maybe just a little)
Addressed a clogged catalyst. (this was noticeable compared to when it was clogged)
Fixed the flapper under the air filter to always stay open. (no noticeable difference).
Run one quart of marvel mystery oil per oil change. This provided a noticeable decrease in blowby. I catch the blowby oil vapors that separate back into oil in a catch can and return the oil to the crankcase manually. So I know from one week to the next how much blowby it has.
I monitor inlet fuel pressure to the injection pump using an aftermarket Dodge Cummins fuel banjo bolt that has a pipe thread in the hex. Same thread pitch and diameter as the Mercedes. It is: BANJO BOLT - TAPPED - 12MM FITTING ('89-'93 and '98.5-'07, 5.9L) @ $7.00 quite a bargain. Place is in Cumming, Georgia. Kind of ironic, town name so similar to the products they carry...

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Turbo300Mercede
87 300D W124
83 240D W123
80 300 TD Wagon W123, 4 Speed from 79 240D, SLS Rear Suspension

Yes, the cat! Jake, are you able to run a straight pipe for testing?

Umm... my '87 300D was pretty quick without touching the full load stop. There's no way it could keep up with either '98 E320 which I think run 0-60 in the low 7s

You're probably running out of breath because of (IP?) timing. Tweaking the full load stop should help some but take small steps if you don't have overboost protection.

Sixto
98 E320s sedan and wagon