Yeah, it's not the most effective method and does take longer. I know there was a thread about baking by material id's and some exploded mesh script renderhjs was working on.
there is a script for max4 and up, on scriptspot http://www.scriptspot.com/download.asp?ID=1069 that allows mass changes to keys, but I would think there might be something better in max7
the weld works, but only within it's threshold distance. I'm not sure where to change that in the default unwrap window though, but it is in the sidebar list with the chugnuts uv tools script.
Turn off isoline display. I wrote a little script that replaces export/export selected. It just turns off isoline and then exports. simple but a life saver.
Why do you need to do that? It should be possible to make a script to save the lightmap(s) after baking and then reassign them after baking the other set.
In 3d studio max go to Script > listener or hit F11 then select all objects and in the white field delete everything and type : deleteModifier $ 1 and hit Enter.