Any fault codes? Check Engine Light on? You should be getting a P0700 which indicates problems in the transmission. You'll need to have a shop with an advanced drbIII tool to retrieve the transmission fault codes. Until you find out the fault codes, it will be very hard to diagnose. Any reputable shops in the area?
Did you change the fluid and filter in the "new" transmission before swapping it in? All electrical connections secure and clean?