Well I just remembered why my WE was so high,I had raised war taxes... I think that solves it 
I'm also playing a ERE game, and I also get big rebel problem.
I think these things affecting this problem most in my game:
1, high Infamy and bad relation with other nations (so they keep sending spies trying to screw me up)
2, high WE
3, low stability (cannot fully recover it to +3 after modernization, bad events keep push it down)
It's not like those rebel can kill me, and I can easily defend myself against any other big blobs. However, the game just become ultra tedious as I can do nothing but rebel hunting for years, and I have to micro-manage it all the time. The auto rebel hunt feature generally won't work as I want it to. For example, my east african army will try to go all the way to Asia minor to hunt the rebel there, while leaving my African province unprotected. It only seems to be helpful when the defeated rebel bouncing around. My vassals help me a bit (I like to create several big vassals), but it is not so reliable either.
I've never got into economy problem with ERE though. (I still have 0 inflation during 1550-ish)