Before I tear into it, chasing my suspicions, please let me know what you think the problem could be and why.

Car: 1986, 300 SDL (OM603 motor) 181K miles

Situation: the worst symptoms started just after installing all rebuilt injectors (new nozzles, pop pressure adjusted). Also, on the test run after installing the injectors, I found the crankcase to be over-filled with fuel, which turned out to be due to the fuel return line sitting over the open injector hole for two weeks with fuel dribbling into the cylinder and past the rings due to warm temps and resulting pressure in the fuel tank, AKA "the incident". (Full saga here: http://www.peachparts.com/shopforum/showthread.php?t=298078) Now I've done two oil changes in 50 miles and am running Mobile 1 full synthetic for diesel.

Symptoms:
-At cold start-up, seems like it's running on 4 out 6 cylinders. Smooths out after 60 seconds. Did NOT do this before I installed the rebuilt injectors and the "incident".
-Idles LOUD, which noise 'reduces' (not gone) above 1700 RPM and whole engine is virtually SILENT when throttle lifted and slowing/coasting all the way to stop, whereupon the noise resumes. Hard to pinpoint where the noise it's coming from, but stethoscope basically says the whole top end and not one cylinder more than another. While not as loud, this noise was present before injectors/"incident" and was the reason for doing the injectors in the first place.
-At idle and fully warmed up, the car shakes like it was my old 300SD/617. Before it's fully warmed up, the idle, while loud, is fairly smooth. But not as smooth as other 603's. This symptom was present before the injectors/"incident" but not quite as pronounced.

Just fixed/replaced/checked:

-Glow plugs. Put two new ones in and tested the other before the injectors/"incident".
-New, fresh oil, as above.
-New air filter, intake clear, turbo spins fine, EGR plugged, ALDA adjusted and lines are clear.
-New fuel filters (both).
-Catalytic converter eliminated (as an issue)
-Compressions BEFORE the 'incident' were 360-385.

I 'suspect' that new injectors with increased opening pressure may be revealing late timing due to stretched timing chain or some other reason. But am also concerned that I could have caused some other unknown damage that is causing these symptoms by running the car for 1 min (less than 2K rpm) with 8 quarts of oil PLUS 8-10 quarts of fuel in the crankcase. So perhaps the next thing to check is the compression, in case poor lubrication caused scoring of the cylinder walls or valve damage(??).

Whaddya think? What should I check?

__________________
1986 300 SDL, gray on black, #14 head, 180K miles
1982 300 CD, silver on palomino, 290K+ miles [sold]
1980 300 SD, white on palomino, 500K+ miles when retired [uncle's car - inspiration for the above]