Herbaciarz,
Thanks for noticing this post. The final fix for the clinking and clanking was setting up the front and rear differentials. They were both VERY loose. Both driveshafts had about 5/16" of free-play. The third member in the differential was slopping around about 1/16" side to side. After the rear adjustment, the free-play was heard but not felt, or felt but not heard. I forget now.
The cause of it was excessive idling in gear that slowly widened the free-play. Diesel engines have a lot of torque from each cylinder-detonation that rips through the drive train. The automatic transmission doesn't have a flywheel like a manual transmission, so the roughness of the engine is not smoothed -- it's as though the crankshaft is square. This is the Flexplate for the automatic transmission. It's made from about 10 gauge steel, not 3/4" thick cast iron like a flywheel. I would like to see this plate made from 2x or 3x thick steel to provide some real flywheel action.
The rear differential was pretty easy because it's adjustable with inside-the-axle nuts to set up the placement of the ring gear to pinion gear. To gain access to the adjustments, you only have to remove the rear wheels, brakes & axles. I set it to 0.005" play but I later learned from a machinist it should be 0.002" for a used set of gears.
I had to make a huge hex driver out of a 1/2" drive socket and a huge nut to turn the 36mm (or larger) hex-drive nut inside the axle. Here it's only epoxied together but it worked. There is not any real torque needed for this adjustment. (Adjusting the pinion gear lash is a different story)
The front differential is adjusted with spacers -- I haven't actually done the front yet, but I did remove the front driveshaft. To gain access to the front differential adjustments, you have to remove the front wheels, brakes, take out the top ball joints, remove the bottom of the strut (the yellow part), and then remove the half shafts.
These things quieted the vehicle down real nicely. It's a nice car to drive now -- however it's not quite back on the road yet. Just sent out the Engine Control Module for repair. I suspect I'll get it back by mid March.
You have a lot of work ahead of you, and the justification to buy a lot of new tools. Good luck whether you do it yourself of take it to a shop.
Dean.