Replacement Engine For 2006 Gt

I have a 2006 GT Convertible and it has come time for a replacement engine (220k and has a blown head gasket or a cracked head). I have been looking at rebuilts and used and its getting slim pickings for 05-06 4.6L with lower miles in salvage yards. I know that the heads and other parts were changed in the 2007 model year, however could I have a complete salvage 2007-2009 4.6L dropped in without any issues?

Thanks!

I was looking at dropping in a complete engine with harness, its more the harness to the BEC that was concerning me. From feedback, it looks like I would be ok with dropping in the complete engine.