Robert, you need to talk to these guys. They'll know and won't give you grief for wanting to mix and match Ford parts.
http://groups.msn.com/FordFlathead19...3/general.msnw
I don't think the flathead tranny will bolt to an FE engine without some machine work. Also, if I recall right, they don't handle hugh amounts of torque - they were built for 110 hp.
You might want to re-focus on world class T5's or mid-80's 4spd OD from F150's
Tim