Spoke with Ford today. They will warranty the parts - I pick them up tomorrow.
1 Lifter, 1 Head gasket, 8 Head bolts (must be replaced). The engine came with a rather nice lower intake gasket that amazingly released from the RTV. The gasket itself if better than anything else I can find and the part that Ford lists is not the same, so I am going to re-use it (was only on the engine for a short time).
FWIW, Ford did tell me I could just put it back together and take it to a dealership, in which case they would cover the parts and labor. Seems like more of a hassle and time, so I declined. They also said any future problems with the engine assembly are covered, parts and labor. I knew the engine came with a 3 year unlimited mile warranty, however I did not think labor was included since I did the install myself.