WOW, you are really picking up the clues I've been putting down! This is the closest anyone has been to figuring out the plot, but I can't confirm or deny anything right now.
I would say there is a clue you have discounted/missed, which is that Maya was also getting letters asking her to come to Bluecorp 2, but she thought they were TV license letters and threw them away....
Will keep your nitpicks in mind!
All tracker stuff is subject to a rework, I want to add sound, a notification if there's a tracker scene available that you haven't seen, and maybe some text, but it's gonna take a lot of work, so I can't really shoehorn it into an update easily. It will come in time though. Hopefully it'll all feel very natural by the final update, I can even change the progression around as I see fit. :]
Also, the model in the sex scene is the same model I used in the Maggey falling art, and is consistent with her in game body dimensions, but I totally see what you're saying. I don't like Phoenix' dick in that scene either but it's still good enough, and pretty fun I think.
To address the NTR related comments: I'm just trying to make the very best lewd Phoenix Wright parody/homage I can using themes I enjoy. The game won't have a sad/bad dark ending, and there will be a lot of laughs along the way. It will not be a super long game, I estimated 2-4 hours originally. Also I respect Maya and Phoenix as characters and will not do them dirty.
Thank you all for the kind words. :]