i believe the Si master cylinders were always bigger than the regular models. (15/16" versus 13/16" i believe....) so no, you will want to go with the bigger Si model.

as for DOT4/3, they should be compatible with each other, so i wouldnt worry about that too much... if nothing else, the fluid will work as a test medium to find your other problems. once u get those straightened out, you can drop $10 and pump the whole system clean with some fresh DOT whatever you want.