I've also had the experience of not doing well on the fly, switching to spin gear and hooking up much more frequently. It is frustrating, but I think it has a lot to do with the distance you can cast with a spinning rod.
One thing that makes a difference for me is paying attention to being stealthy when the water is low and clear. When wading, I have more luck when I move slowly and deliberately to a spot I want to fish, hitting that spot and moving to the next. I've been reading Clouser's book on river smallies and Ken Penrod's smallmouth book (mostly focused on spinning for them) and both of them emphasize casting to targets. Picking those targets can help the spook factor. Clouser talks about the importance of long casts for the same reason.
Along those lines, stopping my cast a bit high so I don't slam heavy Clousers or crayfish down helps me, too. Though I have had times when slamming poppers down is what they want. But if that's the case, you'll know it. I was listening to one of Tom Rosenbauer's podcasts on smallmouth and his guest, Colby Trow (2014 episode), talks about sometimes needing to "outslow" the other fishermen, just letting your fly drift with minor twitches. He also said he'll sometimes pop his popper after the initial splat and let it sit for 15 seconds before doing anything to it. That's something I haven't tried yet, but it's worth a shot. I'm usually too quick on the retrieve, I think.
I'm far from an expert at this, but those are some things that might help. Definitely tips I need to work on as well.
Check out the Orvis Podcast with Tom Rosenbauer, that one from 2014 is really good for smallies. Bob Clouser's river smallmouth book is also well worth the time. I'd also check out Eric Stroup's two-part video series on the Susquehanna with Bob Clouser. He gives some really useful tips.
