I think that one might be a bit past what the scripting can handle easily (when you read the special rules, you'll understand). That said, it's easier than you'd think - each floor uses the same map tiles, at least.

Ah, hm. I tried setting it up, but the map tile seems to have snap points assuming that the tile is rotated 90 degrees different to how it's set up in the map, so monsters, objects, etc, snap to the wrong place on the grid. Is there a way to change that?

TTS has a setting for the grid to be rotated 90 degrees but the snap points might still be off. You could try "Options"->"Grid"->"Snapping" to "Both" and try the different hex grid types.
PS. we played this scenario recently and did not have this problem.

It probably is luck whether that happens - if the last scenario you played had the same grid orientation, it'll be fine, and if not, you'll have to change it.