Thank you for the replies and info. I took it to a transmission shop for testing and they said that this transmission has aluminum pressure plates and the one for 3rd gear is bad. The guy who did the test told me that when they replace them they use a ford transmission with steel plates that will last a the life of the transmission. Options are to drive it until 3rd gear fails and replace it then, or replace it now. He said that I will keep getting the check engine light intermittently, it's off right now. Only drawback I can see to waiting is the CEL for the AT issue could mask something else, but I think it's a pretty low risk.
