jacksbike

Well, you have hit upon most of the problem points. First of all, I would not run the upper pully wheel without the 2 dust covers. Try to find another SunTour used rear derailleur that you can utilize its upper pully wheel. If the chain continues to fall off the upper pulley wheel, you either have an alignment problem, as you have noted, or the upper pulley wheel has a lot of movement in it.
Suggestions (some of which you have already done). Make sure the rear derailleur frame droput is aligned correctly. Make sure the rear derailleur is perfectly vertical. Make sure the rear derailleur cage is not bent. Make sure that both pulley wheels are the same , so that your current upper one is not spaced closer than the bottom one. Check both rear derailleur cage plates-some obstruction ? I am still convinced that the problem is either lack of pulley dust caps , too much side to side movement, or incorrect spacing of the upper pulley wheel. There really is no other reason why the chain should fall off the upper pulley wheel. Good luck.