Ok so here's what I've learned about your questions.
The ML map replaced map0.mul They are the same but ML doubled the dungeon section of the map.
You should go ahead and create a black space from y:0 x:5119 to the bottom right of the map, regardless of wether you are using Fel or ML map sizes because the server automatically wraps th map a few spaces to the left of point x:5119. Any places to the right of this on the OSI map were accessed via teleporters and conatined the dungeons such as Shame, and special places like The Lost Lands, Jail, and Green Acres.
The maps by MUL are as follows: map0.mul=Felucca, map2.mul=Ilshenar, map3.mul=Malas, and map4.mul=Tokuno. It's a misconception to believe that map0 is Trammel, Trammel has no map. It shares the same .mul as Fel however the .dif and statics files make them appeare different. The reason I know it's Fel and not the other way around is because when i first began playing UO way back in the day there was only one map. Fel, Trammel came later. If Trammel did have a map it would be map1.mul since it was the next facet opened to players.
As far as editing current maps go I may be wrong in this and Punt or Dian can coorect me in this if need be, but I believe you can edit a current .mul map with world forge mapeditor... Though if you want to do heavy duty land reshaping you're better off just creating a whole new map for it.
To create your map, start with the terrain map and the pallet/swatch for it, then after you get that like you want, go into mapgenerator, point the terrainmap directory to that .bmp, place the correct map sizes in the box, change the atituted entry to reflect the altitude map name if so needed, then go up to Generate>Altitude. This will create the initial Altitude.bmp you need to work with being sure to change your swatch to the altitude swatch. Make the changes you desire in there, save it, go back to map generator, change the paths to refelct the .bmp files as in the steps to create the altitude map as before, then click Generate>Map. Viola, map made, you should have three new .mul files.
Now getting those .mul files to show in game is another story... and making certain changes I'm still learning myself.
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