Well, I know why my antennas are supposed to be a little shorter than the simple formula says, the patch cable to the duplexer is acting like a transformer. What bugs me is the extra 1/2" or so I have to trim to hit resonance. I can't figure out where it comes from. I have a decent transmission line model so I'm assuming it's in the PL259 or in the NMO on 70cm, even though they are supposed to be impedance matched to 1GHz I just don't buy it.
On your other issue, this is something I preach, lip and fender mounts distort your signal patterns, especially with 1/4λ and 5/8λ antennas. You lose about 3dB compared to the center of a roof in the plane direction and will have very little signal to the non-plane side.