You can get the SN95 master cylinder and keep the Fox booster, but it'll be stiff. You won't want the Fox master cylinder whatsoever. The way you worded your question it's tough to see what you're really asking, so that should cover it.
My car has had the Fox booster/SN95 master cylinder for 7 years and it's fine, but I'll be swapping to the SN95 booster soon.
which master cylinder you use depends highly on which front brakes and which rear brakes you run.
Master cyinders are sizes to specific ratios dependant on fluid volume requirements of the calipers, so there is no "one size fits all" master cylinder
I was too...but which SN95 MC to use depends on front calipers. Cobra, 94-98 GT, 99-04 GT or try and make the stock fox 60mm ot 73mm stuff work with SVO rotors and Sn95 rear disk.
So 5 combos....3 different SN95 master cylinders to pick from
I did the 99 GT brakes all around with PBR's and braided lines. I still have the stock booster/master with perfect and I mean like stock pedal and awesome stopping power. Don't know why it works but it does.
Don't use the fox master cylinder with rear disc brakes.
I did that and it felt fine. Then I got bit in the butt ,, The rear pads are gone and the fronts look good.
There's a check ball in there somewhere and it don't like disc brakes.
Trust me on this one.
That would be more a cause of the combo valve. More than likely a failed/seized residual pressure valve in the rear of the prop valve. The MC does't have any sort of check valves in it
Main difference is the bore size. Disk/drum MC's are smaller than disk/disk because drums require very little fluid to operate. While the stock MC may work, it's grossly undersized and requires a long stroke to move enough fluid. In other words, may braking performance is prob being achieved at nearly the end of the stroke.
I've always recommended MC/Booster selection to be idential to original car the brakes came on. Use that as a baseline and then size up/down 1/16" depending on stock or SN95 booster and desired pedal firmness