[john]

I wouldn't worry about the smoke as black can be rich or lean.
rich - unburnt fuel
lean - burning the carbon off the tops of your pistons

Brake pads and cel are not related problems. The cel probly had something to do with your bov but I have no idea why it cleared itself.

Idle surge can be:
-Base Idle Set Screw (need new oring or new screw). Check by seeing if it started backing it out
-your vented bov can cause it as my hks and blitz did
-vaccum leaks
-bad ISC motor