Thanks so much for the invaluable wisdom. I've got the accelerator arm about right with a little trial and a lot of error, and fixed the vacuum pump with a piece of thin-walled tubing and some silicone.
I am getting a lot of black smoke on acceleration that I didn't have before. I never touched the max fuel screw so I think this is timing related, but I'm not sure which way. The engine also seems to have more knock/clatter than before above 2000. The power seems a little flat off the line like there is more turbo lag, but that could be my imagination. The engine starts very easily without any smoke.
I set the timing by the wrong mark initially, which caused a little bit of valve/piston noise. I just now fixed the cam timing (took me 20 minutes, I'm getting good at this!) but I didn't have the gumption to get right into fixing the pump timing. I set the pump by the before-TDC tooth on the flywheel, so that would cause it to be advanced, but I think I might have had the cold-start on, which would have a retarding effect. Maybe they canceled each other out, but that would just be too convenient.
In short, engine noisy and (black) smokey; is the timing advanced or retarded?