https://photos.google.com/photo/AF1QipMhMV-F7rGX01RVs-AaM0r_kKvcNCIOnJOG65FS   

Grrr.  Linky not happy.

You can leave it rounded and put fillets on it to transition the opening to the inside walls. That would eliminate the ledges.

What kind of rasp are you using? A Shinto rasp should take care of the corners in 5 minutes or so.

Finally, if it's not too late, i.e., you haven't glued the trunk in yet, you could define the problem away by making the trunk go all the way through the hull and putting on a fiberglass "scab" to protect the endgrain. Details on how I did it for my schooner are here, but it should be applicable to the skerry. Note that you need a slightly longer trunk than the plans call for if you do this.

Good luck,

Laszlo

  Mine shows my lack of previous experience at least as much as yours shows your deep expertise! I was using an old fashioned wood file/rasp.  It works, just a bit slow.  Also, I really left a lot of margin on my saw cuts to remove.  Looks ok now, if not perfectly square (or rounded) on the ends. Now on to the interior fillets...