The '87 and earlier most likely had the smaller master and booster. The '88 and later most likely had the bigger master and booster.

Swapping parts will change your brake power and feel for better or worse, depending on which parts you use. Here is some related info:

http://home.4x4wire.com/erik/4runner/brakes/#Basics

'97 4Runner, '06 F350, '86 4Runner, '05 WR450
http://home.4x4wire.com/erik