Yeah hang tough...the skunk can be a streaky fellow. It starts to mess with your head and affect your confidence, but you know what you're doing, so just keep after it. IMO the best way to get rid of the skunk is just fish the flies and techniques you have the most confidence in and are most comfortable with, regardless of what's happening on the stream.
I was the benefactor of a training conference at work wrapping up early yesterday so I was able to get home in time to sneak out for an hour. Took home my usual skunk courtesy of the Quittie DHALO section...and it was just stocked last week! Had a nice fish on, but never even got it up out of the depths to see what it was before it threw the hook. My last several trips out I've lost over 75% of my hooked fish to poor hooksets or just plain weird stuff like the fish wrapping the tippet around a small twig and shaking off. It happens, don't let it affect ya.
Your watershed may have been hurt worse than some others with the floods last Fall too, or it may just be in a bit of a down cycle now. If it fished really well last year with lots of nice sized Brookies, it makes sense that it may fish poorly for a year or two once most of that good year class dies off. Normal ebb and flow of small wild streams.
As far as the stoneflies go...I see them all the time in the Winter on many of the streams I fish and the fish never seem interested in them, even on warm days. Not sure why that's the case, but I'm not suprised you struggled even though they were hatching like crazy.
Although the thermometer would beg to differ, it's still Winter, and fishing is still tough. Give it another month and things will pick up.
