JonT,
Did the air cleaner check out ok?
Air and exhaust restrictions can cause symptoms you've described. (hard starting, low power, black smoke)
These are the instructions for removing the fuel injector pump on my Deere 4100. (Yanmar built)
First the clip and washer, if removable. (washer may or may not be fixed to linkage) Disconnect governor linkage, remove mounting nuts and washers, then pull injector pump straight up, lining up pin with notch in housing. Dont pry or otherwise damage timing shims or housing. Same number of shims (thickness) removed to be replaced using protective seal coating.
Replacement reverse of removal (but of course) /w3tcompact/icons/laugh.gif
Reconnect governor linkage using hole closest to front of tractor.
Use engine asy lube to help hold washer in place.
Bleed fuel system. Using same thickness of shims timing normally should not change.
Maybe it can help. Maybe not.
Anyhow that's how its done on mine.
Good luck
DFB