My game was running super slow as well from the very start (At Irenicus' Dungeon). Now, I have wayyyy too many mods installed and my overes in thereide file was like 1.2GB so I figured that's the problem. I cleared up a lot of the files in there, took the overide down to about 850MB but the lag still remained. I removed SOS, but that didn't helped either. Finally I removed the first component of the Big Picture (the AI fixes and all) and voila, lag's gone. I reinstalled SOS, my current overide file is about 1.4GB, I have limitless Bags of Holding and a tons of other supposed possible lag causing mods and my games now run great at the highest performance.
I don't know why, but it's the BP that's causing the lag for me so until the next version's out, I'm not installing it anymore