First, the old flooring was actual teak and holly sole which rotted if not treated when rain water got in. This is going to be lengthy so read gents.
When removing the teak and holly sole, it is usually glued down and you need to clean all the old glue and any sealant you see. I would suggest ordering from Hunter as they have the floor plan as they now use the marine laminente which is basically a plastic material that no maintenance is required. When installing, you will need to trowel the glue all over and then put a cloth cover over it and place weights down to adhere to the glues. Let it dry overnight. Then you will need to put a bead of silicon around the perimeter to seal the edges of the floor. If you find any bolts or screws underneath, then something is amiss as that is a solid glass floor acting as the top plate of the water ballast tank.
If rain water is coming in around the top sliding hatch, then you will need to remove the hatch and take out the lexan. This is a two man job and do not attempt to do this on your own. There is a board on the top at the back that goes across. Take it off and clean off the old caulk. Replace with a new bead of caulk across the entire bottom and screw holes. Then do the other two boards the same way. Then put it back on. Do not pressure wash even with a hose as water can get underneath the hatch into the cabin floor. I would suggest that you get a cover that goes over the hatch to cover that and make sure you put a cushion under it or on top of the lexan slider to angle the water off. You can order this thru this website.
Water under the cabinetes can be from anywhere. If you take the boat out and drain the tank, then put alot of red cool aid mix down into the tank and then put the boat back into the water. If the water is red, then you have a tank lid leak.
If the water is not red, then it is coming from topsides. That can be a dilly to find. The easy way is to close the boat and put tape over the forward hatch where it comes down, close the opening ports well and then tape a large plastic piece over the entire companion way. Then slit it big enough for a leaf blower and insert the leaf blower and tape that off. make sure you have a bucket of soapy water and brush. Turn the blower on and in essence you are pressuring the cabin. Then brush every fitting, hull to deck joint and so forth and where there are air bubbles, there are your leaks. Good hunting on the leaks
Crazy Dave condon