Perhaps it's a one-way chain.

Is the RD moving when you shift?
Try running through the gears without the chain, see how that setup is going.
The SRAM comes with a master link, so it's not the normal Shimano pin failure.

I'm not confident that the chain size difference of .004 makes a whit.....

Replacing the chain is primitive and simple. Re-running cables/housing after a repaint, now that's a more likely scenario for an issue.

Are you going OK then "losing" a shift? Almost sounds like a housing caught on a ferrule, a cable guide snafu, or a cable not sliding well. I'd double-check the entire cable route, each connection and ferrule, make sure all is OK in that regard. I'd also make sure the shifter was "zero'd down" when the cable was inserted (a common error on STI's, not sure about MTB's...).

If you can't fix it, I'll pay shipping, and you won't have to worry about it.