[Kyle]

Personally I would scratch or use a sharpie and mark the exact location before freeing up the motor mounts.

Then free them

Then install the new engine.

I took my DD engine and tranny out. Replaced the entire engine and set it back in. Doing this did not require adjusting. I guess I'm lucky but when I set the engine into the boat and bolted it down the shaft fit the coupler to the tranny perfectly. No binding, or off center issues.

I also replaced the block so I was shocked that there was no adjustment needed.

So loosen the mounts to where they can be adjusted. Do not adjust them though from where they where when you removed the engine. Install engine. Tighten or loosen the adjuster as needed for the shaft to align freely mating perfectly. Tighten set but.