Waterproof the alternator with one of the proprietory sprays, it is simply sprayed into the alternator internals. This will give additional protection, but follow the instructions, and do not rely solely on it.

To fit a winch: it is recommended to fit a second battery suited to the winch, this saves the engine from stalling if the battery becomes flat. Connect this using one of the many digital battery management systems now on the market, many give a battery condition inside the cab with a digital display. These replace the old split charging systems, they bias to the engine battery, but utilise any surplus power for charging the auxilliary battery.

To fit a roll cage means fitting a solid bracket to the chassis and fitting a base plate flat under the floor, from this manufacture a top using a top baseplate, and fabricating a top to your specifications. This forms a sandwich with the vehicle floor and prevents water ingress, but ensure your welding skills are good if you intend using it for protection.
Steel tube to the correct scecificationis available from steel suppliers, along with bends at various angles. I would also recommend sleeving the joints with a smaller diameter to increase strength of the welds.