You have to decide whether you are going to make the cockpit sole sealed and self draining. It will then have to be above the waterline and glassed in all the way round. The alternative is to have a removable sole and water will drain into the bilge underneath. You will then need a bilge pump and a cover for the boat otherwise it will fill with rainwater. Either way you will need to glass in transverse floors in the hull to support the ply.
Be wary of taking the cabin off. The boat depends on the top for stiffness and if you remove the top you will probably need to strengthen the hull and remaing deck to compensate.
don't know if there is one were you stay , but the last floor I put down was from a recycle yard , floorboards from an old building , well weathered , painted with deck paint and then varnished >
What I did with my trailer sailer floor in the cabin was to fill all the voids between the stringers etc with mix em up foam carved it smooth and laid fibre glass over the foam. Now I am not sure this was such a good idea. It did give me added head room inside especially as the floor could follow the stringers etc to some degree so while not flat did give most hadroom. Unfortunately I did not use enough glass and after a while cracks appeared which then allowed rain water etc into the foam. Cabin windows are never water tight.
I did add more carbon fibre for more stiffness. What I would do next time is fill the voids with foam then cover witha wax so that I could make a molded floor out of carbon fibre so that it could be removed for drying out and cleaning underneath.
However for the cockpit area there is much to be said for a self draining cockpit. ie a floor above water level with drains to get rid of spray or rain. Especially important if boat is left ona mooring. good luck olewill