Below is a link to a long posting I made 5 years ago about various sizes of master cylinders and how well they worked with my XJ's brakes system.
I just updated it to reflect the present usage.
http://www.naxja.org/forum/showthread.php?t=991378&highlight=master+cylinder+diameter
My XJ presently has ZJ discs, in the rear, and 15" Vancos, with the larger 48mm calipers, up front, as well as the ZJ proportioning valve and a stock master cylinder. It will lock up the 33"s at freeway speeds.
At present, I'm thinking about an adjustable proportioning valve for the rear brakes. With the powerful front brakes, there is a lot of weight transfer to the front, lightening up the rear and
allowing rear discs to lock up in wet conditions, even with the ZJ proportioning valve.
Grand Cherokee can take full advantage of their rear discs since they all have ABS, which prevents lock up.
My present thinking is the ZJ brakes are not all that useful an upgrade if the front brakes are being upgraded. Drum brakes, in good shape, might be all that is needed.
Discs are easier to work on, never need adjustment and stay cleaner in muddy conditions.