Hi: The first time I worked on a Volkswagon diesel I had a problem like yours, and I was stumped. Not running good at idle, noise, black smoke out the pipe. It must of been by the grace of God that I tried pulling out the cold start advance that it was equiped with. ( the engine was warm and I was going down the road) It advanced the pump 21/2 degrees. What a difference, I couldn't believe it. The car took off, good power, no more smoke. I went home and retimed the pump, solved everything. Might be worth a try. I know it isn't easy to get the timing right with the 1 drip per second method, try to advance it a little. I usually make a mark across the block onto the pump, then I move the pump a little, about 1/4 inch. If it makes a good difference your on the right track, if not try 1/4 inch past your mark the other way. If it doesn't help set it back on your mark, recheck the valve clearance, if that don't fix it maybe someone has an idea for you. I find great help on this forum all the time.

Good Luck