Engine for 06 V6 automatic-what will work 05-09? Difference between auto & manual
 

05 V6 automatic. Considering replacing engine with another 05 or later 4.0 V6.
Fordparts.com shows different engines for automatic and manual. Considering a used one and don't want to be stuck with a half ton of junk. What about differences in later engines 06-09. Will they drop in or is there a difference in wiring harnesses and other things?