With your difficulty getting the mastercylinder out of the throttle assembly, did you remove the two , allen head fasteners that secure the m/c to the throttle casting ? They can be missed easily, if you're not familar with it.
If so , there's a good chance you've got corrosion in there.
If you can do this, there is a snap-ring that holds the piston and seal assembly into the m/c itself, if you can get the snap-ring off you should be able to remove the 'innards' from the m/c.
Don't be too surprised if you find corrosion damage inside the m/c bore.
If you get lucky, and all you need is the normal wear parts, they are readily available.