I suspect you placed the hammer as "tile" - but it is actually not a tile but a sprite.
So you have to add it using the sprite tab. Somewhere on page one I wrote that the editor currently does not filter the tiles list...
Multi-tiled items are "in game code" only represented by the top left tile, the others are added "on runtime" and overwrite tiles which might have been placed there. That is the reason why the editor works with 16bit tile indices when the GB only uses 8bit. (All indices > 0xFF get "deleted" on compression/insertion)
As for picking up the editor again... (Did you came here because of my post in the Zelda2 for GB thread... ?)
I think what threw me of the project last summer was the inconsistency in the sprite attributes section. The game has quite some "left over" bytes in there which makes it very hard/tedious to determine what bytes actually make a difference, what is the "default value" etc...
I think I will push this part back and try to debug the "switch code" sometime soon(TM)
EDIT: Hm I somehow missed the question about the ladder/floor blocks...
I have to admit I don't remember whether I tested them, but I *think* just adding them as tiles should work?
Also I feel honoured you joined to post here
EDIT2: It seems I have not fully woken up... You already said you came here because of the lack of speedruns... When I worked on the editor I also thought the game would make an interesting speedrun - there are some many moves/tricks Mario can pull off.