Great work Jeff. I agree it takes an inordinate amount of time to do but it is essential maintenance on an old M6x.
If it isn't smooth and everything else is as it should be, the idle fuel flow or spray is often at fault in one or two cylinders of an old FI motor- so your injectors may need a proper clean to sort this out. Here in Oz our fuel is generally clean (and low-sulfur) but at this age you can still easily get one or two injectors with fouled valves or a poor spray pattern.
Also, I might have missed it, but did you install new plugs?
I did the same with a set of M60 valve covers off a wrecked 540 I have here. You'll be pleased to know that those of us with RHD cars are not immune to the same sufferance when removing the right side valve cover, thanks to the *&$%! positioning of the e34's AC plumbing.
It won't make you feel any better but when I removed a cover I remember loosing one fastener too.
I cleaned mine with fuel and then cheap spray 'degreaser' (some kinda acid) and as the donor car was not in use, had the luxury of leaving them to soak for a day between rub-downs. It took perhaps three goes and stripped the paint in the process- but I didn't notive much alloy dissolving. inside the covers wasn't bad though, oil had not caked the covers too much (it had 310,000km), probbaly thanks to the central PCV design. After that I sanded and filled the castings and filled the surface pits where they were most obvious. Then etch-primed, primed and painted with high temp silver. I dunno who BMW got to cast these covers but you would be forgiven thinking they were done in some gulag in Russia or Northern China where quality takes a bit of a backseat to survival.
The set off the wreck seemed to have all good threads, but the set they will replace on the good car sound like yours. I reckon the cause might not be the castings disintegrating as much as the coil nuts getting overtightened every time a mechanic takes a look hoping to solve some fault or 'smoothen' it out a bit. If you think about it, if the studs are even a little too tight each time it goes back to a customer, the cast alloy threads will just disintegrate over time given the constant change in temperatures they go through.
The threads holding the plastic covers were the worst however, which makes sense as those probably get tightened by successive owners every time they start cleaning their pride and joy under there.
The trick with an M60 is probably not to use synthetic oil as the valve gaskets are only butyl. It is possibly that BMW have upgraded the OEM gaskets to viton as they did on the M52 and M54 motors, but I'm yet to find out about it.