you are using indexed housing yes? the housing isn't getting chewed up somewhere is it?
This is an important thing to check. From your description it sounds like it could be a cable issue. Remove the shift cable all the way and inspect each section of housing. Also make sure your cable routing isn't causing kinks which will degrade shifting.
Are you SURE the RD is sitting straight? You mentioned straightening the hanger. If it's not straight it could cause the jumping you describe.
Yes, it's shimano SIS housing - cut with good cutters, burrs removed, opened with a sharpened spoke. Ferrules on both ends - seated properly.
The housing loop is plenty long to avoid the sharp bend that 90% of peoples' bikes seem to leave the shop with
....at least that I notice.
One thing I noticed in the work stand is that in each gear, I can still move the shifter a little and the RD does actually move to a noticeable degree....meaning that each time I shift it there's probably some latitude in where exactly the shifter stops. Maybe this can cause the chain to occasionally try to "pop" over onto the next cog while still shifting pretty well and seeming OK a lot of the time. I guess I need to figure out the best cable tension adjustment (even though it seems to index pretty well over a fairly wide range of barrel-turning).