Is there any way to completely remove elevation, or even change the elevation is a single room?
Lusternia is such a pain to map.

Lusternia is actually easier, overall, than other IRE games to map.

You can change the elevation of rooms you select (shift-click to select multiple) with the Ctrl-M macro (or Edit -> Move). Change the Z value and then drag the rooms to where they fit with the rest of the rooms on that same elevation.

Personally, I like that Zugg's mapper puts rooms on different elevations, and it makes my maps a whole lot easier to follow. I only move the occasional up/down room when it's not a true elevation change in the game.

I say it's a pain because of places like the Inner Sea.

There isn't any way around getting pushed about is it? (can't fly, unless someone will let me borrow their Faerie Wings)

Actually... if you some form of trueswim... or waterwalk... you won't get pushed around at all... just so ya know.

Even the Totem ability Trout will help you there.

Waterwalk doesn't protect you from the waves! LIAR