I would drill the holes a little bigger, also go to the other side of boat and drill a hole over there, tilt Bow all the way up as high as you can get it and let it drain for a few days.
The rot stuff that you saw is for rotted wood, not no wood! So I think forget that at this point.
I guess at this point I would fill solid with 5200 and let dry for a few days. It will harden up even under water so this is why I think the best way.
You could also leave the 5200 am little reaccessed and when dry cover with marine tex for a solid cover.
Thats what I would do I guess, see what else oters come up with.
Good Luck
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1986 V20 
Old Fishermen never die, we just SMELL that way!!
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