Messing with maps...

Didn't the work Madsiur did with expanding/relocating map data fix most of those questions? I don't remember off hand how/why, but I seem to think that solution solved at least one of these questions directly.

Second, I don't know how far you've dived into it, but keep in mind while your deleting to make room, some maps are full of "junk" tiles that are called by several different other maps. I seem to recall several shops doing this, calling trash looking tiles from the "Blackjack, backroom" map (which is one little room and a full map of random tiles).

Just a heads up if you haven't noticed it yet. Removing random tiles may leave unforseen holes elsewhere.