That's impressive you converted and alpha to a bravo! The bravo's are for the big boys
Can the bravo really handle that much hp that you are sending through it? Man that is a lot at 630!!!!
It is a bummer having to drop the lower unit to change the impeller but that's life. Is the bravo version on the engine side easier to change?
As you guessed, the old man had done one of two things, probably both. One is never aligned the engine and the other is crank the engine with the stern drive in the full retracted position for towing. There is not a cut out for it and as you know the universal joint will lock up but the engine will still turn over.
I did buy an alignment tool from this site. I also got a new stern drive from SEI. No way can I afford a new mercury and rebuilds never last. Here is a useful link for manuals if you need.