I am acquiring a 30 year FHA Non-occupying co-borrowers mortgage loan with a family member. However in 2 years I would like to remove my Dad and add my wife to the deed. What are the downfalls?

A lot of people add and remove people from the deed to their property, without any trouble.... but if you change title the mortgage company CAN accelerate your mortgage (make it become due & payable) if they find out. If you remove your dad from the Mortgage or Loan and add your wife she will have to qualify for the mortgage with you. You will have to do a refinance with your current lender (or another lender) you will have to have a new appraisal & credit docs to prove you qualify. If you do a "Quit Claim Deed" or "Gift Deed" adding your wife and removing your dad. He will still be responsible for the mortgage until he is removed from the loan and she will not receive the credit for the mortgage payments on her credit report until she is on the loan.