I plan to lightly sand the areas and then apply silicon.
Is there anything I have missed?

Silicon is useless as a sealant if it is a keel stepped mast. You need a need a mast boot or use mast boot tape as the deck joint has too much movement for silicon. Have a read of the attached article.
www.cruisingworld.com/how/reader-tip-no-more-leaky-mast/

Water can also come in via halyard exit holes. My boat has the base of the mast in a well with an automatic bulge pump just for the water that comes down the mast.

There's an episode of RAN Sailing on YT where Johan adjusts a mast drainage hole on his Beason 40 -
Interesting part starts at around 9 minute mark. It may not be relevant to your issue :)

I thought he drilled a second hole just higher than the original and then pumped in resin to seal the expanding foam (which was a bad choice.)
I guess if you don't use the manufacturer-kit then the option is, after you run a generous diameter conduit (for your cables), you fill the mast at deck level using a non-absorbant foam, maybe you could expand a flat balloon or plastic bag, waxed or PVA'd before injecting resin or similar on top, withdrawing your balloon afterwards. Whether its worth going to all this trouble I don't know.