Skuzzy,
Tried it and no go.
I made a *.awa file using the current (old) cloud tool and placed it in my TE2 terrain folder, and then opened TE2 and built the terrain. A *.awb file was created but was blank so I know the editor at least looked at the *.awa file. The resulting *.res file was the same size as the one without clouds so I don't think it worked – I also loaded into AH2 but found no clouds.
As you mentioned, the format for the *.awa file has changed. Unless we can see an example of a good .awa file, we're stuck until the new tool is out.
MachNix