I was able to get to the 2nd or 3rd stage on the 5th level before I hit a wall with the Delete function. It was actually working really well for this game until that stage for some reason.
UPDATE: I re-uploaded a new 3DN. After the problems I ran into later in the game it seems that some of the basic stuff I had done early on were un-done. The new 3DN shouldn't have any problems until the 5th floor now.