Hi Scott
After installing S5, I see ClickToFlash is compatible. Only problem has been with CosmoPod.
As you suspect, it might be a router issue. Which router are you using? Have you unplugged/waited/plugged in the router, then restarted the computer/Safari? If not, try that and see if the loading sequence returns to normal speed.
I'm using a dual band Airport Extreme. My load times are very fast - faster than Safari 4.0.5. In case you are using an Airport Extreme, have a read of this
this recent MacWorld article.