You can't go from one extreme to the other. You wrote the first letter saying that you trust her. You can't flip-flop to the other extreme with this "I checked up on you and know you are lying" letter. So, you sent the first letter, which was too extreme in that direction, now what are you going to do?
You can print more than one SW boarding pass. i've done it before. That doesn't really mean anything. Besides, by printing it she checked in for the flight, so that seems to confirm that she was still planning to go to Phoenix at the time she printed it. And only an idiot would throw it away in the house if she were planning to fly somewhere else. i think she went to Phoenix and ran the race. Do I think she met a lover there? That possibility exists.
As to your statement that a lack of trust will undermine your marriage. You are 100% correct in that. Trust is essential, as is forgiveness. I think you can non-chalantly ask about her trip and get answers to some of your questions. But showing that you did your own detective work will be harmful. This is a longterm thing. If she is having an affair there will be other signs, you don't need to confront her when she comes back from this trip.