well first off I don't believe that the car would even start with the MAF unplugged (at least with the 1st gens I know they won't run with their VAF's unplugged, for sure), but if it did, I can hardly see how the MAF (mass airflow sensor) could cause the transmission to go funkey, mabey its just that your A/F ratio is all screwed up with the MAF unplugged, and the car is going into safe mode (thats assuming that the car would even run with it unplugged).
Do you have a digi Cam? if you do take a picture of your engine bay and show us what you unplugged, im pretty sure it would be your MAF since thats the only thing the Air filter would hook up to.
I have a feeling you don't really know what your messing with, so your best bet is to leave it alone and study up on your car and how to do the performance mods correctly. Im not trying to be an ass but if you screw things up doing the Easiest performance mod one can do, then you really need to study up on how to do these thing more. (i just don't want to have you screw up your car and cost yourself a tonn of money trying to do performance mods that you didn't learn how to do yet)
In the mean time we will try to help you get her running properly again.
Now here's what I want you to do, take a picture of your installed intake (take a few of them with some close up of your installition), so I can see your installition and check to see if you did anything wrong. then if everything seems fine, I'll tell you how to reset your ECU so the car can learn the new mod.
If the car still dosn't run properly, check the plug on the MAF...make sure you didn't damage anything. if the plug seems fine plug it back in...and make sure its making a good connection, if it is, and the car is still running like crap, take you new air filter off and reinstall the stock air box back on excatly the way it was, the try the car again, if the car still runs like crap, then Im pretty sure your MAF is broken and you should replace it. If replaceing the MAF dosn't work repost in this thread and othe people will help you go from there.
I hope I helped a bit.
methman