Replacing Top on 1930 Tudor Sedan

[gypsycandle]

Upon removing the top material and the two piece rain gutters which were still in great shape: I found only one mouse hole in the top which i repaired. The chicken wire and under lying materials are still intact and in great shape.
Now my question is what type of sealant are they talking about in the instructions ,"place a bead of sealant under the rain gutter before reattaching"
Question two: what do i used to fill in the tacking holes along the gutter's path, some of the wood is rotted on the very outside (but not on the inside). I cannot replace the wood because the interior was just completed.
Any suggestions are appreciated. Coming to the end of my two and 1/2 year project now.
thanks in advance,
Michael...