1999 Honda Civic IAC or transmission?

Hi.I have a 99 civic lx 156000 mls auto. On day when driveing the car started to make a whineing sound and when I stop the car would shack and feel like it was driveing in a low gear and would some times not go when I would come to a complete stop, just rev.I would have to cut off and restart the car to go then the check engine light came on.(This all startd in the winter). Problem stop for about a month or two then one cold night it startd doin it. Iac or transmission?
ps. For a short time a took off the air box tube that gets air from the front of the car and just had the box that sits on the top of the throttle boddy. Could that have done some thing? Thanks so much for your time.