Disagreement is welcome, especially when done respectfully as you have done. Thank you, sir.
I think you are right, but I am skeptical of making the solid place for the plugs to hold. If it is a bit too wide or a bit too flexible, the plug may blow (even with the mechanism closed). I understand most plug blows are from the mechanism failure. I fear it could also happen if the port is a bit too wide or too flexible as well.
Of course, I could be wrong. This is certainly a first for us...
I would say it may be luck of the draw. You can try CoPart... But the other thing is you may not need an exact match. Yamaha used that same setup on a whole range of boats. My '12 has the same thing. So you actually have many years from which to choose. You need to find a goodly wrecked or burned boat where that back pump part is undamaged. If you go that route, make sure to take pictures of your extraction from the donor boat. Not sure how the tube is held into the fiberglass, but there is probably a lip or something there and pictures may help them reconstruct.
That said, do heed
@Beachbummer 's (and many others') opinions here. My idea is far from easy or cheap. Certainly not a sure thing...
I agree this may be a viable option. Hate to see you do it and lose the cleanout ports, tho. I agree with
@Julian that your base looks ok (it is above that where they destroyed things) and you could epoxy in. Only problem is that will likely be irreversible (without doing my original suggestion, that is). So you may even want to try the welding option before you go for the epoxy option. If you do try the weld, when you test it, put a nerf football in the hole after/on top of the plug. If it does blow, you don't want it to come up with full force against the hatch and ruin it.