The Hydramatic engine can be used with a manual tranny as long as you find a flywheel and bellhousing to fit. You will need to check to see if the crankshaft has been drilled for a pilot bearing. If not you can either have a machine shop drill one or swap out the crankshaft. I've heard that some were and some weren't.
However, the converse is not necessarily true. Hydromatics were matched to the engines. To get a hydromatic to work properly it has to be precisely machined to fit the block, therefore they are a matched set. If you still have the transmission you may be able to sell the set to someone who needs it and have enough money left over to get a nice running 261.
I know the cab floor cover is differant for the hydromatic, and there should be no hole for the clutch pedal. Don't know about the frame, but the engine will be fine.
