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Broad Reachin'
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Sounds like you're on the right track. In any case, here's an excerpt from Don Casey about installing a new deck hatch, but with a similar procedure which might be helpful:

Seal
When you make a cutout in the deck, you nearly always expose the core material--either wood or foam. Because water finding its way into the core has such disastrous consequences, it is imperative to properly seal this raw edge. The bedding under the flange of the hatch is not adequate.

Dig out a half inch or more of the core material all around the cutout, then sand the interior surface of both skins. Saturate the exposed core with unthickened epoxy. Thicken the remaining epoxy to peanut butter consistency with fibers or silica and fill the gap all around the cutout. When the epoxy cures, the core edge is permanently protected.

Fair
Lay a straightedge across the deck just beyond the cutout to assess curvature. If the deck is not perfectly flat, you will need to fabricate a spacer that matches the deck curvature on the bottom and is flat on the top, or you will need to build up the deck around the cutout with epoxy paste or fiberglass laminates. Grinding down the crown is almost never an option because it further weakens a deck already insulted by the cutout.

Normally a hatch's metal frame provides adequate reinforcement to compensate for the weakening effect of the cutout, but in the case of large hatch, especially one mounted in close proximity to other holes through the deck, some additional reinforcement may be advisable. This usually involves structurally framing the hole, either with wood or with additional laminates of fiberglass.

Bed
Dry-fit the hatch in the cutout and drill the pilot holes for the screws. Mask the deck all around the perimeter of the hatch with Long Mask--the blue masking tape. Mask also the flange. You can let the tape stand vertical; its purpose is to keep sealant squeeze-out off the frame. Remove the hatch and completely coat the deck between the tape and the cutout with sealant. Use polysulfide if the hatch frame is metal. For plastic hatch and deck plate frames, you will need to use silicone, or a silicone/polyurethane blend (Life Seal).

Install
Put the hatch back over the cutout and wiggle it gently to distribute the sealant. Insert the screws and snug them all. Now tighten them, following a pattern of the next screw in sequence being as opposite as possible, i.e. right side, left side, front right, rear left, etc. Do not overtighten the screws or you will squeeze out all the sealant and the resulting metal to fiberglass joint will soon leak.

Finish
Let the sealant cure for two or three days, then trace a razor knife around the perimeter of the hatch frame to separate the squeeze-out from the sealant under the frame. Peel up the tape from the deck and the excess sealant will come with it. Remove the tape
 
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