A 52 331 will have the extended bell housing cast into the engine block. That will put a limit as to what transmission you can use. You will probably be ahead of the game to have the trans that is now attached to the Hemi rebuilt or replaced with another like it in better condition. A 52 331 Hemi in a stock rebuilt condition makes 180 HP at 4200 rpm. That is less HP then the currently available V6 engines, but is 77 HP more then the 49's original flathead 6. How much more HP your supped up flathead 6 makes might surprise you. With having a modified flathead 6, I'm not sure a 52 Hemi will be much of a step up, considering the effort involved it getting it there. A 3 carb flathead 6 is almost as impressive as an old Hemi under the hood.
At minimum, to change the flathead 6 to the Hemi, your looking at: motor mounts, exhaust, wiring modification, inner fender modifications, a transmission for the Hemi, possibly a driveshaft, and a lot of work. The process will involve removing the hood, radiator, inner fenders, pulling off the front sheet metal, removing the flathead 6 and its transmission, modifying the frame to adapt the new Hemi motor mounts, fitting the Hemi and its trans, modifying the wiring, remounting the front sheet metal, installing a radiator capable of cooling the Hemi, modifying and reinstalling the inner fenders to give side clearance for the Hemi, and having an exhaust system made for the Hemi. I'm sure I missed something, and any time you speak Hemi, the price of anything doubles, even the old low power versions.

The flathead 6 motors were pretty good motors that were capable of moving the cars along quite well. They were not race cars, but not dead dogs either. The fluid drive transmission flat killed the power from them, and the rear gearing turned them at pretty high rpm at highway speeds. There are several modern automatic transmissions that can be installed behind the flathead 6 that will perform well, probably the reason the guy you got the car from was adding an OD transmission. I would that the one you have rebuilt or replace it with another in better condition. You will have a nice cruiser that will be a fun family ride.

As far as the other upgrades mentioned above, they do tend to happen. I would suggest an upgrade to the 12 volt system though. Gene