I remembered this thread from when elmariachi was having trans/FE install problems.
http://www.clubcobra.com/forums/fe-talk/95556-427-fe-tko-600-mating-question.html#post930732
ng8264723, you really need to pay attention to this because it can be a really big f***ing deal. The trick is that there can be a problem with the length (and mating) of the input shaft and the bell housing. Sometimes you have to remove
almost four tenths of an inch from the pilot end. If you don't, and the lengths are wrong, you can kiss the thrust bearing goodbye.
In fact, I woke up in the middle of the night and thought of this and added it the list of things RodKnock doesn't know.