Capt. T,
338 came from the factory with an OB well. What appears to be an extra large hole is what it looks like after the box or collar or sides of the well were removed. It was ground back even further when it was discovered that the hull mold was made with the OB hole - you know, like the deck mold was made with the hatch holes in place - but just a flange - and the well sides added later after the deck was attached to the boat.
Also ground that flange away which was gel coated and incorporated into the joining process. Didn't want to rely on old polyester pasted onto gel coat. The well also looked like later alterations had been done.

I felt the Yamaha 8/4. had to be custom fitted because it's so big and heavy.

What was below at the bottom of the companionway in 338 and in thw way of any access were the stubbed off factory straight-thrus and later added seacocks with hose etc. Is was C'Pete who pointed out the many connecting points (that can go wrong) like clamps, hose, valves etc. I committed early on to continuing with the OB and wanted the space below the c'pit for stowage. Drains went out the back.

When Capt. Brent thought about putting his batteries under the cockpit, I thought it a great idea. So batteries where the BETA diesel would go became my plan - I have the flush deck access hatch for the c'pit. The framing under the cockpit for the bats and rather large hatch will create substancial strength and rigidity.

The long answer

Hope you are proceeding with your upgrade!!!!!