I have a 1997 Mercruiser 5.7 carbed, non vortec cylinder head, Alpha One, Gen2 in my boat currently. I purchased a completely dressed 350 Gen + EFI engine that was in front of a Bravo 3. I would like to keep my original engine fully assembled, sitting off to the side. Will the flywheel housing and coupler from the engine that was in front of the Bravo 3 work ok on my Alpha? The alpha coupler is triangular where it mounts to the flywheel, and the bravo is a round plate. If I have to swap the flywheel housing and coupler from my alpha to the new engine, I will, but if I don't need to, I will just leave it together. Thank you in advance

You can't swap a flywheel from one engine to another unless the engine is internally balanced which yours are not. The flywheel is balanced to the engine it is on.
You should be able to take the flywheel housing off the old engine and bolt it up to the new engine and drop it in the boat.

You don't need to swap the flywheel. It stays with the engine. But go ahead and swap the coupler and housing. The flywheel housings may be the same, to verify you can look up the apps in the Mercruiser parts pages.
The main problem will be that the Bravo efi controller does not have a provision to operate the shift interrupt on the Alpha. If you really need to run the engine you will either need an Alpha efi controller or put the carburetor, intake manifold and Alpha controls on the gen+.

NHGuy - does his engine still have a single ignition coil. If it does couldn't he just use the Alpha interupt switch to apply a ground short to the negative side of the coil. I am not familiar with the newer Alpha engines. It has been 20 years since I owned one.

I believe the input shafts are the same size - I know i used the same alignment tool for alpha and bravo setups.