Summerkidd

I have a 2001 legacy gt limited. I replaced a blown ej25 engine a operational engine I purchased from Lkq. I had no prior transmission problems but since engine swap the AT Temp light stays blinking continuously and the check engine light is on. The car does run but initially shifts hard in 1st 2 gears. The hard shifting does clear up after driving for a short distance. Have done numerous code checks and Subaru dealership had replaced transmission temp sensor. Still having problems and apparently the certified mechanics can't resolve this issue. So basically the AT Temp light blinks continuously, the check engine light stays on continuously. Car shifts hard initially than clears up on own after a few minutes . So called certified Subaru mechanic ran computer codes on it and said it was a temp sensor and code showed a -77 degree transmission fluid temp. Replaced that sensor $490.00 later and still little or no improvement. Is there a real mechanic out there that can help me?