Well, I found the problem: MasterController Integration. I removed it after a tip from someone, and everything is fast again now.
prerrrrret Are you using the MC compatibility add-on along with the other Smooth Patch files? That doesn't actually work, in the sense that it doesn't ensure compatibility, and was removed from the upload a while back. MC Integration should be fine with the Smooth Patch overall as long as the compatibility add-on isn't present, but perhaps you ran into one of the issues for which the compatibility part was created.
I also want to reiterate that when the game works fine without mods, but doesn't work with mods, the problem, or at least part of the problem, is one of your mods. I said that earlier and meant it. If you'd tested without your mods in the first place, and taken the results seriously, you'd have saved yourself a lot of time.
