Tyler,
How long was the boat in the water prior to midnight?
You said; "it seems to have stabilized/stopped for the time being". Did you pull the boat out of the water right after that? Or was it in the water for some considerable time after and no more water accumulation? Sounds like the boat is still in the water, is that correct?
Since you are new to the boat and maybe water ballasted boats, it seems likely the ballast tank valve and plug may not have been tight.
Tell us more about the "chemical toilet". Is it a fully self contained porta pottie? Is it MSD? Is there a thru hull valve?
I'm really curious to learn the explanation for what happened. That's a lot of water, 4-5 inches in the cabin
How long did it take for the bilge pump to pump out all that water. At least you know it works good!