On my 2003 29'Fever, where do the cockpit floor drain holes drain out to.
With the boat on the trailer I ran water in them and saw no water coming out in bilge or out the boat? Wanting to make sure its not filling up in the boat somewhere.

mine drain into the engine compartment

If it weren't frickin freezin here in the Pacific Northwest (storm coming in - possible snow) I'd back mine out of the garage and see if I could answer your question. I'd be surprised if the water went anywhere else but the bilge. I can tell you that more than likely you have three bilge pumps, two in the engine compartment and one under the first step leading into the cabin. My cabin pump seems to be an automatic version as it has no off/on switch or visible float switch.
I'm curious as to your top speed? I've read anywhere from 75-80m.p.h.

My 47 drains into the engine bilge. I hope your hose is not cracked and draining somewhere else. Do you have 2 drains?

If anything like my 27 and 32, they just drain into the hull along the outer stringers and then into bilge. Mine weren't sealed when they drilled the holes, so I hit them with some resin and reinstalled the drain covers. Found a lot of debris left inside the hull during the build that would plug/obstruct the drain holes. Probably the wood from the drilling of the floor drains and such.

Depending on how high you had your bow, might not have had it high enough to drain.

I took the stainless cover off the drain and it doesn't go straight down, it seems to go towards the rear and there is no hose that I can see. I know it isn't draining in the engine compartment but I think it should. I didn't check to see if it goes to the bilge under the step in the cabin but I will next weekend, I just repainted the engine compartment so I need a few days for it to fully dry thanks guys.

Yes two drains, one on each side by rear seat.

My cockpit drains to the outside stringers in front of the batteries as well. When I wash my cockpit floor, I notice I do get water on top of the fuel tanks. This worries me. Does anyone have a drawing or picture of what it looks like under the floor of these boats? I also get water under the cabin step and would like to know where it's coming from. Maybe the Fountain Boys have pictures they could share with us!

Water under the steps where does it come from? That is a old good question lots of mixed responses some say rub rail which I'm might believe. rw40426, I would agree with US1 try rasing your bow.

You may be right I will check again this weekend, but I had laid the hose over the drain when I checked last time and still didn't seen any water coming out.