Doesn't Beta Marine have a drop in replacement for the Atomic (BOMB) 4?
Thats what I would do:
Atomic Four Replacement - Beta Marine diesel engine using high performance Kubota diesel, Atomic Four, atomic 4, repowering
But again as others have discussed, you'll never get the value out of the installation. If this is a particularly nice, clean bristol O'day, then do it if you plan on keeping the boat forever.
I, on the other hand, would put up the boat on Craigslist with your current outboard and then scour for a different boat...one that had been repowered already but the owner needs to sell. You'd be amazed at how frequently a boat like that comes up for sale. In the end, you'd let the seller eat the hit of depreciation for a repower.