What shifting issues are you experiencing? Front or back or both? Hard to diagnose without lots more details.
The shifting issues I have specifically as possible is I shift, the gears shift, and all seems ok for a second and then a clunk. After the clunk its staying in gear but feels like it skipped teeth at the clunk. Or sometimes when I shift it's a clunk and teeth skipping right on the shift. before settling in the gear. It's such a big clunk I run through the gears to see if there's been a skip, but no skip so far. All rear gear changes. I'm trying to reduce variables by not even switching the front. The clunk happens under heavy load and on flats under minimal load, and also with different gears. Seems to happen unpredictably. This would make me think bad derailleur or teeth on rear, possibly chain. Whatever it is the chain isn't being placed properly and making such a hard shift I'm concerned about breaking the teeth. Teeth look fine (so far), cassette is clean.

1st gear is still a little noisy due to cross-chaining. Again, this is to be expected.
This is interesting, I might have unreal expectations. Maybe I'm expecting seamless gear changes, or wondering if this is possible with an upgrade.

Thanks for all the replies!