Did you simply bolt the 727 to the engine?
There is an .060" difference between the Hemi and the LA/Magnum motors, if you lack a spacer this may be the reason for your interference. Thus, a .060" spacer is REQUIRED to use a 904/727/518 transmission. Some people get away without the spacer because there is enough tolerance that SOME transmissions bolt up without a problem. Though it sounds like your one of the unlucky ones. :(
Hope this helps.
Regards,
Joe Dokes