We are sorry to hear you had a hard time installing the door. Regrettably if you are placing the panel in a sliding glass door with a crooked track, issues created during the installation are due to the sliding glass door itself. This is not something the door can resolve since the area it is being installed into is not within normal expectations.
In regards to the issues you have mentioned with the magnets not connecting, this would indicate the flap is installed either too high or too low. If the magnets never make contact, the flap is too high. If the magnets make contact but the flap bows out of the door frame, the flap is too low. In both situations, you can loose the flap installation screws and adjust the height of the flap as needed. Doing this will the draft issues you have noted around the pet door.
If you have any further questions or concerns, please do not hesitate to reach out to us directly at 1-800-732-2677. We are always happy to help!