Hi Mark, I've been watching you're build from a far. Great job, awesome boat.
I have some questions, ideas and checks that maybe helpful. Some maybe redundant, as I don't recall all that has been done. 1st would be questions on you're equipment. Are you getting you're tach readings from the boat tach? Is it set on 6cyldr? I know the tach in our boat is not accurate. Is you're timing light a basic strobe light only? Better lights contain a tach and advance/retard buttons and are generally a little more helpful with the issues like you are having. Now for the motor. Look at the easy checks 1st. If it has points, is they dwell set within spec? When you rev the motor with the timing light hooked up, do you see the timing advance. If not, this could be you're issue. If it does then i'd check total advance while on smooth water. You would have to do research on what rpm total advance is achived and what that number is, for you're 6cydlr. This is where the better timing light is handy. Fortunately you have another engine which seems to run correctly, and creates a base line, so you can double check you're findings with it. It also allows you to switch carbs and distributors to narrow down if it's fuel or ignition. Also make sure you're exhaust and spark arrestor are not causing any restrictions.
If the dist. Is advancing, I'd make sure both engines are set alike. I know nothing about mercruiser dists. On our mallory distributor the timing advance can be adjusted. We have to remove the top plate that the points mount to, to get down to where the adjustments are made. Hope this helps and good luck. Ken