The shop is in the zone to the right of the entrance zone of Summeredge. And it's the same place where the Summerheat Club is. You should definitely try and work out some of these locations for yourself by exploring too. I'll attach an image to make sure you have the right door below.
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I don't think the savefix works for saves below 4.0. So it might not be possible to completely fix your save file. I have a few different playthrough saves around my computer files, I can give you one if you would like. That way you wouldn't have to start over from scratch.
Xyless has some weird variables/thresholds compared to the other companions. She doesn't actually have a corruption variable. She has submission and affection variables. I generally never free Xyless, as my morality is usually never lower than 15, and if you enslave her you can bypass that requirement to recruit her. (That's not actually mentioned in the guide). For a free "good" ending for Xyless try to get her submission and affection for the player high. It's difficult to raise her affection and submission compared to other characters though. So feel free to use a save editor or Lain's mod.