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They were attached to the back side rails. One forwrd and one aft. They used the top rail to stablize the top and were srewed to the shelf that the rail is attached to. Each had 3-4 holes where a rod or boat hook could go and hang. So you had support tward the front of the ron and back where the handle or the rod would be.
Looked kind on simple and functional. If I see them again I hope to have my camera with me.
The rack that you describe sounds like it is the "Rod Tip Rack" shown on page 7 of the drawings for the locking rod box. (Under "Downloads / Parts Drawings" on this site.) These were used as the front rack, and for the rear, there would be either another of these, or the locking Rod Box. On my Sakonnet, one side had the rod tip rack both front and rear, and the other side had the rod tip rack in the front, and the locking box in the back. The rod tip racks were made of 3/4" mahogany plywood, so over the years, with exposure to weather, the plywood delaminated.
Here's the link to the parts drawing page that it is on:
http://www.whalercentral.com/downloads.php?cat_id=13