Ghost shifting with a nearly fully rebuilt drivetrain I’ve got an old Surly Crosscheck that’s been ghostshifting for awhile now. I’ve rebuilt most of the drivetrain to try to fix the problem to no avail.

I replaced the cassette, chain, rear derailleur, and cables but it’s still happening. The RD was originally a top normal Deore XT 9 speed, its replacement is a bottom normal XT 9 speed. The shifters are Ultegra bar-ends in friction mode (busted indexing). 

It happens equally often when I’m really crushing it and when I’m spinning under low pressure. The chainrings are potentially bent/warped slightly? Their bolts are seized, haven’t been able to replace them. A shop bent them back to as close to straight as possible. I’m wondering if it’s the chainrings, or the bar ends not holding the cable in place, perhaps against bottom bracket flex (I’m 255lbs)?

Thanks for making it this far, I really want to figure this out—this bike has been with me through a lot over ten years, but this problem has caused a couple accidents and I’m shying away from commuting due to safety concerns.
Check the derailleur hanger alignment. If the derailleur cage is not parallel to the wheel ghost shifts can happen.

I'd also check alignment of the rear triangle and dropouts.