Thanks for the help. I downloaded one of the add-on carriers, since chopping through cat files was taking too long, and I got the answer I needed. The Ark Royal and Victorious were missing the lines LandDeckAngle and LandingAimPoint under deck. I added those and used the power of MATH to figure out a good aim point. Also, I realized that the Vindictive was set up so that landings were performed at an opposite angle to how the deck was laid out.
On a side note, I see now why the Victorious was never going to be a good ship to fly Phantoms off of.