I guess the specific issues I am having is calculating and rendering the rooms sizes on the map correctly to their "in-game" counterparts and making sure they are explored at the same rate the player is moving around in the level.
Then rendering the placements of links and borders that line up properly is also a challenge of course. Another complication, that you brought up actually, is I do have offsets when the player leaves/enters a room. While it works great in-game to make sure I can put links at different heights and such, I suspect that it might also make rooms on the map, with their real sizes, would start to overlap each other. Does that makes sense? :S
(I realize now that I am done writing this post that my "specific issues" is more like "the entire map system" )