Re: inline 6 transplant from 1969 to 1982
I know the feeling, and recently did the same.
Which outdrive/housing assembly did you have and plan on installing? I assume you are going back with an alpha 1 Gen 1. If that is the case, make sure you have the room in the engine compartment. The exhaust on the pre alpha routes in between the transom mounts, where as the Alpha 1 Gen 1 mounts are about 5" narrower and the exhaust is off-set to the outside of the mount. Your riser elbow will also need to be changed to offset the dump to mate to the exhaust.
To answer your question will the holes in the transom line up with the newer plate, the answer is no. You will need to fill in the existing and drill new holes. When I did the upgrade, 2 holes lines up, but had to fill in the others and re-drill new holes.
Your front mount may also have to be adjusted. The Gen 1 rear mounts are pushed off the transom about 1/2"-3/4". I had to unbolt the front mount, replace the cross member of the wood, glass it in, and re-drill new holes to mount the frount engine mount.