i am thinking it depends on the year of 4.6 you plan to install. some were designed a lil different. i would try going to www.car-part.com and see if you might find an engine easier to bolt up instead of one that might be different.
4.6 didnt use AOD except early production 1992. if i remember right, it had AODE. the engines should be capable of same bolt pattern as the older 5.0 engines were. i know the 5.0 engines would bolt to AOD transmissions and i think a couple other.