If I didn't seat one of the air box tubes correctly on a carb, would that give me those symptoms?
Yes, it could. Get a small mirror that you can use to look at the back of those tubes. I have one that is on a swivel on the end of a metal rod and it works great. It is really easy to get one of those tubes folded under a bit on the underside where you cannot see it without a mirror. Also, check to be sure you got the tubes back on the air box from the PAIR control and the crankcase breather.
Bigwolf