Master cylinders from 90-00 are 7/8" bore. 01-05 are 15/16" bore. This size does not affect brake balance.
The proportioning valve affects brake balance. Refer to this for factory prop valve specs: http://www.flyinmiata.com/tech/stock_bpv.php
The 01-05 non-abs prop valve gives the most rearward bias of all factory valves, besides the ABS ones which are just straight through.
, brake boosters on all NAs are the same, 99-00 might be larger, and 01-05 non-sport is definitely larger.
I have installed in my car the 02 non-abs prop valve, master cylinder, and brake booster. Some would say the NB2 sport booster is ideal for optimum pedal feel, claiming the non-sport boosters provide too much assist. I just used what I had on hand.
Swapping in the 01-05 master cylinder was pretty easy and only required bending lines by hand. BUT, you would have to swap the booster in with it too, otherwise the pushrod would require lengthening or something. I can't remember.