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Chain length is a good shout. At a push I could remove a set of links. Might make a difference at the high end as the range is so huge it does look pretty slack on the smallest.
Clutch is fine, and I was worried about it being wheel slip so slammed it all the way back to guarantee centering it for a ride earlier and it had no effect.
I guess based on your last point that it could also be a bent derailleur or hanger. Not sure how to test for that specifically other than a hanger alignment tool.
I recently got a secondhand 1x11 setup on my CrossCheck. It's a Shimano xt mech with clutch, cassette and chain with a Renthal narrow wide chainring on a Saint crank.
I find that it drops the chain every now and again whilst shifting, sometimes on non-rough terrain.
My first thought was that it wasn't shifting clean, so I re-cabled it, but that didn't seem to fix it. The chain isn't worn (0.75 on my measurer didn't fit in, not even with a bit of force) and I'm not sure what to check next!