The master cylinder on the Baggy (and your '03 shouldn't be any different than my '05) is a very unique item. It's a Grimeca setup that is apparently unique to MZ (even Grimeca doesn't appear to carry replacement parts for it). I doubt that any other rebuild kit would be useful.
Probably the best thing to do would be to go through an MZ parts supplier. If you're in the U.S. try SF Moto (415.255.3132,
http://www.sfmoto.com/). They appear to still be having good success ordering parts from Germany. If you're across the pond, there's a working parts supplier there (Grahams?). Search the board. There's been a lot written about them lately.
Hope that helps.