I've never rebedded mast partners, but I have rebedded mast steps
on deck stepped boats. The biggest hassle is getting the thing off in
the first place, and cleaning up all the old bedding/caulking/sealing
compounds. For something like a partner (something that you won't
be rebedding frequently,) I might use 4200 or similar. I only use
silicone type sealer for something like the trim plates at the chainplates,
which I reseal every year.
If you partner has through-holes through the deck, it is a good idea to
drill them out slightly over size, then countersink both sides. Put
tape over the bottom hole, and fill with epoxy with enough filler to make
it mayonnaise thick. Check out
http://www.westsystem.com for more
information.
After the epoxy is cured, re-drill the through holes, finish the top and
bottom ends of the 'plugs', and you are good to go. Don't forget to seal
the exposed core in the big hole either!
There should be chocks all around the mast, not just either fore and
aft or port and starboard. The port/starboard chocks should be set
to keep the mast in column. The fore and aft chocks are set (along
with the step position, and forward lower shrouds,) to achieve the
desired mast pre-bend.