Hi Mark,
I've been following along here, real bear of a problem.
On a yanmar, i'm not sure. However, I've been doing a bit of research on this for my cummins. If the pump timing is too far advanced (from what was originally intended), the engine will not run right at idle. However at WOT (wide open throttle) full rpm, it might run fine. Lower rpms, stumble.
Most folks I've spoke to about pump timing won't do it without the proper tools. However, with that said, if you don't have the tools, maybe a two stage test (idle rpm and WOT) will tell you if it is running acceptably? I don't know, just kinda thinking a loud... Good luck, let us know what happens... !
btw, is this on a 1600 series tractor?