Are my frequent Safari beach balls caused by my extensions? Every 2-10 minutes Safari pauses with a spinning beach ball for roughly 10-90 seconds, sometimes asking if I want to reload everything, making Safari almost unusable.

I've installed several safari extensions that mess with pages to prevent cross site attacks, scripting, cookies, etc.  In particular, my active extensions are : AdBlock, ClickToFlash, Ghostery, JavaScript Blocker, and JavaScript BlackList.  Anyone experienced conflicts amongst these before?

Additionally, I've installed but disabled Disconnect, NinjaKit, and WasteNoTime, but presumably disabled extensions cannot contribute to the problem. 

I'll experiment with disabling these active scripts piecemeal, starting with JavaScript BlackList, who's role is presumably superseded by Ghostery and JavaScript Blocker.  

I'm especially curious about whether Ghostery and JavaScript Blocker might be conflicting, given that they do very similar page editing.  I prefer JavaScript Blocker for being infinitely more aggressive than Ghostery, but Ghostery has a better curated block list, which helps me allow stuff through JavaScript Blocker.
I'd say it's definitely possible, if not likely.

For starters, turn off extensions altogether, to verify that they're causing the issues. Then I'd suggest disabling them one at a time (which sounds like you've tried partly), until you can isolate which one is causing the issues.

If that doesn't help (but all extensions off does), then try only one of your Javascript blockers at once, in the event that some conflict between them is causing problems.