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Did the new engine have a flywheel with it? If so, then it probably would have been balanced as well. Regardless, whatever new clutch/flywheel you put in the engine should be balanced as a pair (even if neutral balanced). Hopefully you have some local flathead friends/experts to assist you in what you're doing - so you get the right combination of parts to finish the job and insure they're installed correctly.
You'll need the correct water pumps (believe they're truck pumps) - that mount like the original engine mounted. What I can't tell you is the necessary front of the engine stuff (to fit in a 48 Merc). You need to know what parts to run as far as fan, generator/mount, etc.. Also, if you don't already have a distributor designed for this performance engine, you'll NOT want to run the stock distributor - you'll need an aftermarket one or a custom one built for a non-stock 49-53 engine.