I'm not the dev but I can try to help you out.
1. If you are ever stuck, you can use the debug option in the menu at the top left corner of your screen or use this menu to fast travel. You can also use the "Covert Cube" in your inventory to fast travel.
2. The Ayleen fight not working was a bug that was identified and supposedly fixed in the newer FF release that is now on the site. If you are still seeing this bug in the bugfixed release then that is unfortunate but MTool can be used to skip the fight in an emergency.
3. The instructions should be clearer in the game, I agree. The "Main Quest Guide" on the Katalist wiki has been updated, however, which can be followed to complete the new content.
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4. For this update at least, I have not had an issue with using saves from earlier versions to access newly released content, however, I have heard that saves may be incompatable with the next release.
5. The idea with the Verl encounter is that she will appear every evening (multiple times if you wait for too long) to fight you and drain your levels. In theory, this should only last for a few days as you linearly follow the main quest progression. I have seen some reports of visual glitches like you have shown remaining after completing the update, however, they are intended to disappear after each battle with her.
I hope some of this helps and agree with your ideas of fixing up some visual bugs and letting players start from the new content.