For the cruise control make sure that the cable it connected to the TB. On occasion mine it pop the connect off if I run the 'tour at wide open throttle. Also did the car have cruise control before engine swap? Also 95-97 models differed from 98-2000 models. It might have something to do with the ECU.
For the lower vents, what lower vents??? are you talking A/C and heat vents? If some vents blow and others don't make sure the vents are open because as far as I know there is only one blower under the dash. So if your vents are opened and there is not air flow, they must be clogged.
