Not seeing your stones, I am only guessing...but I suspect that (as you suggested) your poorly cut stones are far better than most overseas-cut stones.
I really don't feel you would jeopardize your reputation by selling these at a fair price, so long as you note that you are a beginner faceter, and the stones may not be cut to high precision standards. I don't like your use of the term "poorly cut". I find it hard to believe that your stones are "poorly cut", even if they aren't perfect or up to your standards. As you yourself state, people have seen them and have been quite pleased with them. I suspect you are selling yourself short.
Truthfully, I have seen faceters who (like me) are excessively OCD about meets and polishes, but I have also seen some (rather well known) faceters who are more into production cutting and cut to nothing more precise than an optivisor.
Regarding your machine, I doubt the index gear is to blame. Sounds like you have slop or run-out in your quill/mast assembly. This may be something easily remedied by tightening some screws; however, it may be fabrication error/design flaw. I'm not personally familiar with the design of your machine.
My own machine had a host of shortcomings, which I have either learned to overcome or which I have modified to some extent.
Also I suspect you may have "wobble" (run out) in your platen. It is also possible you have no platen wobble, but that the platen's plane of rotation is not in line with the plane of sweep of your quill (ie) it may slope from 12:00 to 6:00, or something similar.
It is very common to have some degree of run out in faceting laps, and variance from lap to lap enough to require some cheat when changing laps. Unless significant, lap run out is typically not that big of a deal, once you learn how to compensate for it.
Probably too much info at once, but if your machine is loosey-goosey, you are always going to be chasing errors. A sloppy faceting head is probably the biggest killer of precise results.