Hi , so I've changed my alternator and I'm 100% sure all connections are good. But still 12.5v running at the batteries. I'm assuming my 90A fuse on the starter is blown. Boats at dock and is a huge pain to remove, the engine bay is sunken in the hull so to access the starter I'd need to pull the engine or remove all the left side manifold and exhaust. How can I just make a new line from alternator directly to batteries?? Thanks

Ayuh,.... Run a 10ga. wire from the alternator, to a 90a fuse, to the battery,......

12.5v is not bad. If the batteries are dead they would probably show 14.4V or so, but good batteries I don't believe need the draw on the alternator.
Why would you assume the 90 fuse is blown. Are you not able to start your boat?

I would try to run wire from alternator, thru a 90A fuse and to the engine side of the battery switch and not directly to the batt. This way the batt switch can still be used to shut off power if needed.

What about like this ( my red pen line) ?
would I need to remove the original orange wire from the alternator? I ask because everything works except the battery charging, so I'm wondering if it might feed a few things before the starter fuse.

If I am reading this correctly you have a no-charge condition?
Verify no charge- measure at Bat engine off and engine running. Repeat measuring at alternator.
What caused the fuse at starter to open? Does started operate normally, amperage draw or voltage measurement at rest and while starter engaged? Is the starter pulling too much current?

Per your pic the Org on alt and Red at battery are electrically the same.
EDIT
So the alt went bad and now suspect 90A fuse, can you remove the positive cable from Bat and Alt? Check for a Pos cable somewhere shorting to ground, might explain both bad alt and fuse.

The previous owner had shorted the the alternator by connecting the + and - on the same terminal. So I believe now with the new alternator properly installed and no charging that likely the 90a fuse is blown from that previous error. That said, I cannot reach the fuse on this boat.....

Copy that! That is why the 90a fuse is blown. I had a neighbor kid who was 6' 10" (went on to become an MLB pitcher) who undid a starter bolt for me. I could do it but needed to put on a nylon long sleeve shirt, exhale, and have someone pull me out by my feet. He reached in there and just undid it with no grief. I suppose pulling a manifold is not that bad.

If you are certain of your diagnosis I see no reason you cannot fab up your own cable w/inline 90A fuse straight to battery. No real reason to leave the existing ORG from Alt to 90A fuse on or take it off. I would take it off but protect the "hot" end from grounding in the event somehow the fuse re-made its circuit. You could simply bolt a new 90A fuse to the battery and run a heavy gauge wire from Alt to the other post of the new 90A fuse. As suggested maybe to batt switch first then bat w/90a fuse. You need to buy one anyway....

Does anyone see a safety issue with this?

That fuse being blown would prevent it from starting. The fuse is inline of the red/purple and is there to protect the rest of the boat from doing what he did. The red and orange should be direct connections and would not be affected by the blown fuse I believe. If you unhook the orange from the alternator and check it for power, it should have battery voltage all the time and if it doesn't then there is a bad connection somewhere. Just my thoughts.

with the key on,check the voltage of the purple wire on the alt.should be battery voltage,that is what excites the alt.