Verdant is pretty nice with the authors recommended settings. Not much of a hit either. I compliment this with Unique Flowers and Plants. My iMinGrassSize is 70.
I ran around for a good 2 hours and didn't find a single thing out of sorts with EL + SoL Fences. I certainly could have missed something. I think I'll leave it installed and see how it goes. The variety is kinda cool.
I would go through the mod list one by one and compare version numbers. Upgrade the ones you need to, and start a new game. Not sure that's the best way, but I don't like to do a bunch of work and get in game only to realize I've screwed something up. 4 months is a lot of changes.
I use Birds of Skyrim with the Ruhadre patch. Didn't bother with the rest. Read about some problems with Flocks, dunno about Skybirds. Maybe you should see if your current setup works first eh? ;)