Twin 502 Mercruisers want to be at different angles for alignement...>?

I am restoring the boat. I did a new transom and new transom assemblies on my Scarab 33AVS. Both engines are aligned perfectly with the bar alignment tool and the front of one engine sits about 1 inch higher.

I checked the transom assembly angles with a digital level and they are within 0.1 degrees of each other. The only thing that was unique is the standard double lock washers were too tall on the back engine mounts, so I used shims instead to achieve a perfect alignment, but I don't see how that has any effect. So I am stumped.

New transom assemblies would not use the lock washers but also depends on the bell housing mounts.

Is one hole a tad lower then the other, or stringers higher or lower?

I would check the bushings in the bell housings. I installed new ones this past winter.

raising or lowering the rear mount with shims will raise or lower the front of the engine when using an alignment tool.
Use the exact same shims on the rear mounts for both engines and then raise or lower the front of the engines to get your alignment.
The gimbal bearing will angle to what you need for proper alignment.
I made an adapter similar to what is used on a TRS drive to make sure the rear mount is shimmed properly.
If the transom assemblies are new then as I said just use the same shims on both.

Hello, All thanks for the input. I will share the answer. The engine mounts were worn or damaged. I replaced all now the engines are near exact angles. Cheers.