If you drill the holes oversized a little, then epoxy the pillars in, and at the same time assemble everything the way you want it, it will cure without worry whether it will go together later with alignment of holes. Just use copious wax or other release agent so it comes apart. Be careful of mechanically trapping stuff in the epoxy.
Then come back later and bed the action to float the barrel. I think doing it last will serve you best to make sure it is exact.
Not sure what bedding the bottom would look like. You should get pillars that are they full length so you don't need to bed the bottom metal. At most a skim bed between pillar and action I think, as part of the epoxy bed for the receiver.
At least, that is what I would picture doing.
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