Finally got my 1993 300D 2.5T back on the road last month and running like a top after a timing chain failure earlier this year. (The timing chain failure trashed the original engine and i replaced it with a lower mileage engine). Then lightening hit again....vacuum pump failed at 80mph on I-95. Luckily, no apparent engine damage. Just replaced the vacuum pump and the car runs, but:

• engine sounds bad. mechanic thinks the injection timing may be off and causing it to run rich and loud.
• very low power. It almost seems as though the turbo isn't providing any boost.
• stalls after high speed runs. takes a few minutes of sitting and then it will start right up.
• just ran it for 3 hours at 80mph on the interstate....very low power but runs fine at high speed/high rpm

What could the problem be? it ran perfect before the vacuum pump failed, and with a new vacuum pump on it sounds and runs poorly. Could the timing chain have jumped a tooth when the vacuum pump failed causing mistiming? Could the injection pump timing be off? what else?