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The Wood Locating Diagram says in a note at the bottom:

"CENTER TRANSOM AREA IS 2" PLY. SIDE AREAS ARE 5/8" PHENOLIC FOR AUX. MOTOR & SWIM PLATFORM"

From this it is safe to assume that anywhere you want to bolt the bracket in will have WhaleBoard behind it.

The length of fastener needed can be calculated by adding the 5/8" WhaleBoard thickness and the thickness of your brackets' flange and then add 1/4" for the fiberglass and round up to the next available fastener length.

But you do not even need to do that because once you drill your first hole, you can just probe it and measure the actual thickness.