First, thanks to everyone who took the time to reply.
Quick update.
I moved the boat out of the garage yesterday, and changed the plugs(after cranking it multiple times to make sure there was no substantial water coming in. Left Engine started, no problem. Ran a hose on it for about 5 minutes just to make sure it stayed on. Good to go.
Right engine turned over, then died. Took the plugs back out, cranked it, a ton of water shot out of all 4 cylinders. I panicked. I guess the difference in incline shifted water that was still in the engine. Cranked it multiple times to get as much water out as I could. Reset the plugs.
It started. Even without the hose on, there was quite a bit of water exiting the back. Turned the hose on, ran it for 5 minutes. Turned it off, let it sit for about 10 minutes. Went back out, started right back up, ran the hose on it for another 5 minutes. turned it off (had to leave).
Checked the oil and it still seems fine(although I know i didn't really give it a test). However, there was a quite a bit of smoke coming out from the back of the boat while that engine was running. I didn't get an overheat warning. Curious as to whether that should be expected or if there is a deeper problem now inside the engine that I need to get looked at. Local yamaha service shop is 45 minutes away and 4 weeks backed up.
I have a stainless steel scupper arriving tomorrow, so hopefully i can replace that and get the boat out to run it through a harder test.
Just really worried about taking it on the water if the engine is smoking for whatever reason.
Again, thank you ALL for the input. I would say I would have at least one bad engine by now if it wasn't for this board.