Hi big blue,
Get out your file and some abrasive cloth as well as a bar of soap and "fit" your new fin
into the iSonic finbox.
As far as the tiny crack in the gelcoat, the finbox cassette extends at leas 1/2" in all directions from the actual fin cavity so you should have no worries about anything leaking around the fin box.
The finbox cassette is glassed into the rest of the bottom of the board and is glassed to the deck as well.
A little white touch up paint or nail polish the right shade of white and the area around your fin box will look as good as new.
Hope this helps,