Jimmy your description was not clear and you have the expert on this issue which is why I asked the questions trying to determine what specifically there are other issues.
You are correct that there is a teak piece that goes across the top of the lexan slider which is a stop but due to the design if that piece of teak is not caulked from side to side with silicon to include the screw holes and threads, water will seep around/under that wood and fall onto the floor. I bet the caulking around your flooring is not sealed properly. What has happened now that you have supplied more information, water has gotten under the wood flooring.
The floor pan is one solid piece withone section or the floor area being recessed to accept the teak and holly sole flooring. It should have a bead between the floor and fiberglass edge to keep water from getting under the wood. Now you know.
First, go ahead and order a cover for the companionway, not camper top from the store site on the forum. If you have a camper top already, ask that the snaps do not be installed so you can match them to the camper top. You should ask for the snaps anyway. There is a kit that you can buy to put on snaps unless a buddy has one. When you install make sure you put for example a throwable cushion underneath it to deflect the water.
In the meantime, go ahead and put a cover over the companionway and put a cushion underneath so water cannot get in. better yet with another person, remove the slider and you will see some screws on both sides of the slider. Remove them on one side and remove slider to get to that piece of teak on top. Again, have a second person to help. Once I did it bymyself and if fell on my big toe and that was a six week ouch till it healed. Liberally caulk and remember no acetone on the lexan.
On the floor, soak up the water, and have dry rags and sponge.s Do this until you get no more and let it dry. Some have placed a small heater inside the boat but suggest that one be on board for safety reasons. When completely dry and if salvageable, then remove old seal around the floor and recaulk. You can use your finger dipped in alcohol or spit on your finger to smooth that out. I would put tape around the edges to ensure that caulk does not get on either primarily the wood. I would also treat the wood as well. Hope this helps.
craxzy dave condon