The challenge with high performance hulls is that there is actually very little of the hull in the water when trimmed out and on plane ...
It is imperative that the shoot thru be installed in the bilge that has constant contact with the water at higher speed when the boat is on pad ...
This means the shoot thru must be as far rearward as possible and as close to the keel line as possible ...
When the boat is up on plane you can try trimming the motor down some to stick more of the hull in the water ... If the depth reading seems to improve, it means the shoot thru is too far forward and that part of the hull is coming out of the water as the boat planes out on the pad ...
It is also possible the hull wasn't properly prepared by sanding and cleaning the install area before the shoot thru was epoxied in ...
I've even heard of rare instances where the hull is delaminated at the install spot and another spot must be used ...
The shoot thru should be (should have been in your case) tested before epoxying to test for performance at all speeds ...
Here is more info on proper preparation, testing, and installation ...
http://www.bbcboards.net/showthread.php?t=172972&p=1538600&viewfull=1#post1538600Rickie