I have some questions before I can make a thorough recommendation.

1.  Are you describing a delta pad style hull?  Could you please post some pictures of either the hull or blueprint so I have a better understanding of what we are working with?

2.  This is a glass over wood construction hull?

3.  I'm assuming you are trying to use the Berkeley transom cover?

4.  You are using a Berkeley intake?  Which one, for flat or round keel?

Regardless of the above, I would set the intake as far aft as possible.  Basically, you will end up with 1-inch of keel remaining between the transom and the cutout for the jet intake, for a 360-degree bond.

If this is a wood/glass construction hull, I would strongly emphasize cutting the wood back from the intake by at least 1 to 1.5-inch all the way around the opening in both the keel and transom.  Bevel and feather the edge of the wood all the way around.  Then laminate glass over both surfaces, sandwiching together at the edges.  The beveled and feathered edge should be far enough away from the intake so that the bonded flange sits flat on the glass only.  You don't want water creeping into the wood.  If you have an exposed edge of wood, no matter how well you epoxy the intake in, you will get water intrusion and rot.