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My 2000 has this pipe in the rear birth on the starboard side, I have no idea if it is a factory fitting or done by the PO and I certainly don't know what purpose it has/had. Click on image to enlarge.

It's factory standard. You can run cables and wires from the stern through it. The other end is on the starbord side of the motor well / transom.

Correct. In fact, my steering cable goes thru the larger one.

I can't get over how clean and shiny it is back there.

And I have some wiring running through mine, though my steering and engine control push/pull cables go through the other hole, where yours are.

I have a 2000 as well. My steering and throttle cables run through there.

I'm curious why/howe yours do not. Yours seem to emerge from the engine well.

Can you post a pic of your well from the outside? I'd like to see how your cables connect. Do you find it works well/poorly that way?
Emerging from the stb transom is actually awkward. Not only do the cables get in the way, but they bend at an off angle to attach. When I move the OB up/down, the cables spring back and forth.

It's to let mosquitoes in at night.

I had to plug mine to stop the invasion. I didn't know what it was for but it was the only place I could find that they could be getting in. After that...peace.