The four bolt holes is where the water got in to cause the rot. Yes, drop the mast and caulk around and in the bolt holes. 4200 is a good sealer but it is not very flexible, use something like Life Caulk that will flex with the mast/boat. Use it every place a bolt/screw goes through the glass, to keep water from penetrating. AND, about every 3 to 4 years go back and re-bed all bolt/screws. It will save you a lot in future repairs, like you are doing right now. Note,, straight silicone sealer is not a good sealer as it deteriorates in sun light and salt water.