Some more slow progress... I remade the top cover from scratch with the new measurements. It's accurate to .01mm or less (everything is millimeter when it comes to 3D printing).
Here's a look at the top with the caps and the plugs in it. I have it turned yellow right now just for visibility. As you can see, I have the optima sitting inside with the terminals poking through.
Speaking of the optima, I ended up buying one so I rebuilt that entire battery from scratch to be exactly the size of the one I have.
Looking underneath, and getting the angle perfectly aligned so everything is even, even though it doesn't look at due to the illusion, but it is all even... It fits really nicely inside the top cover. This gives me hope that the rest of the battery will fit as is and I'll actually not have to modify any dimensions to get this optima to fit.
Taking the plugs and the caps off, you can see I'm using two studs that will correspond the holes under the caps to perfectly position those, and I decided to actually make it so they plugs can screw in just like the original case. I even offset the screw threads so when the plugs are tightened they are at a 45° angle like the original case.
But one issue that could potentially be a problem, is the terminals sticking out. Because the original case has these three cells that rise up above the top flat area of the battery, the terminals might not rise high enough. I'm going to measure the CW moss battery cables tomorrow and see how tall they are to make sure there's enough clearance. And the photo below, you can see the top flat area of the optima will stop at the red arrow, and the top of the terminal is the green arrow. So you can see how much is covered by the yellow top still.