You can usually see the cracks, typically in the "valleys" between the accordion folds. I've seen it fixed with duct tape, but the long term solution is a replacement. It would make sense that this happened during your major project, because the pipe gets damaged when removed.
I've heard of these symptoms occurring with a cracked intake hose. It's the long rubber/plastic "pipe" from the air filter to the throttle body. Worth a peek anyway. Good Luck!