Update:

I had the injection pump rebuilt and it looks great. I was really happy with how it turned out. Its installed now, but I'm still having trouble timing it. I think I may be a tooth off on the injection pump pulley or something.

I also pulled the turbo and am sending it to a recommended shop in California to be rebuilt (thanks Mike Warme). Once I had the turbo pulled I discovered that the impeller isn't spinning as freely as I had recalled. There isn't any play, but its difficult to spin. Which would explain much of my power and smoking problems.

Once those are in I'll start saving for a 4D56 head and new injectors. Hopefully that can wait another 6 months or so, I'd like to put money into the paint next.