Could be the ECU trying to get settled, at least that would explain the surging with CAI...but it may be the same problem for you try resetting the ECU...like you said it doesnt do it as often now, probebly cuz the ecu is slowly adjusting itself, well speed up the process and reset it

Also what they said about vacums could have somthing to do with it, when i did mine it was weird when one of those hoses was out, but it was fine when i put it back in, maybe you missed one.