Woke up this morning to finally see what lag everyone's been talking about. It's been running smoothly for a week, worked fine last night, and all of a sudden it's hitting a brick wall. Reboots don't fix it, and actually seem to make it worse. So I think CM10 really does just not like you messing with its system apps.
More info: SuperDuperWipe'd, flashed CM10 11-13 & 4.2 gapps package in one go, then booted and worked on changing my settings and replacing MMS.apk & Google Now.
I might try just a regular old install of CM10 next, but does anyone know if just installing the 4.2 keyboard causes issues? I love that thing.
EDIT: Powered through the lag to get to USB so I could copy over CM9 files for an install of something a little more stable, and once I got there and turned USB storage on my phone did something that looked like a crash and reboot. Showed bootanimation and then when that went away my USB screen came back up and lag was gone. What. Is. Going. On.