Can someone tell me if this clip looks right or should it be flush? It seems like the heater core should be about 1/2" shorter in depth for the clip to fit flush to screw down. The heater core is 2 1/2" thick which everything I read says that's the correct size.

I have a factory original Harrison out of a 68 a/c car, and it is 2 1/2 inches thick. and a non a/c core that is 2 inches thick. If you bought it from one of the generic parts suppliers like NPD etc. you are probably getting a one size fits all Camaro nova first /2nd gen part. If I were you, I would call one of the smaller Pontiac dedicated suppliers Like AMES and ask for a measurement. If you can't return the incorrect core, you can look around for the correct clamp for the a/c cars or modify the one you have.