it could be the impeller in your water pump if you have raw water cooling. It could be blockage in intake hose to water pump or a hose from water pump If boat is older, it could also be manifolds. I had same issue and wound replacing manifolds/risers/elbows.
I have a single 350 on a 2010 Sundeck 260 & had the same problem. Manifolds and risers were replaced due to blockage from water/ rust build-up. That fixed the problem.
Could be the impeller for the alpha 1. but don't take anything apart yet before checking the water pressure. It could well be the same problem like MDM with the water blockage. Mine was the riser blockage and water pressure would show higher psi. Also compare your engine's readings between the two engines. good luck.
I have a 1979 with 350 and pre alpha. Had the same problem. New impeller fixed it. I figured it’s the easiest place to start and cheapest fix. 45 minutes and $20 part. Easy!
Sorry for late answer to post but I had health issues for all the advice....I decided to replace my shift/throttle cables because of stiffness and age and am replacing the lower shift cables also. I will be removing the outdrives for this and will replace the impellers and Gimbals and bellows. Hopefully this fixes it, if not then I'll tackle the engines.