One of the givens with keel-stepped masts is the potential for leaks around the partners at the deck. There are many reasons for the difficulty of sealing this area - the shape of the mast, it's extruded channels for sail tracks etc, the relative shape of the deck cutout at the partners, the presence of wedges to position the mast in the hole and so forth.
There are commercially available pour-in-place 2 part rubber compounds (such as Spar-Tite) that can be used to seal the gap around the mast. An industrial compound called Devcon is another alternative although it tends to have strong adhesion tendencies. These products can be poured around the mast once a temporary seal has been made inside the deck. Some care must be taken here to ensure that the seal doesn't leak down the mast and into the cabin while it sets. Precautions also need to be taken to ensure that the mast will actually come out at some future time, don't pour things in a shape that will not pull out, and don't use a product that will strongly adhere to the mast or partners. You might be able to use a mold-release wax to discourage adhesion while still providing a seal.
Of the several boats we have owned in recent years, one had a normal elliptical mast section in partners that were rectangular - a difficult transition to make and we had leakage there for some time. Finally we made a paper pattern and sewed a tailored, velcroed cover out of sunbrella and taped the top of the cover to the mast with rigging tape. We also siliconed the sail track extrusion to prevent leaks through that area. This worked well for us, though eventually the sunbrella will have to be renewed.
Regardless, even once a watertight seal is achieved around the partners, there is still the issue of water finding its way to the keel step down the inside of the mast, due to the various holes in the mast for halyard and wiring exits etc.
One of the down sides of keel stepped rigs!