Absolutely no problem with the master cylinder size running ST205 four pot fronts and SW20turbo single pot rears.  As for redrilling a disc to 4x100 EVERY time you replace it, that'll be what? Once every five to ten years unless you use insanely abrasive pads.

Not sure I updated this thread, but I ended up putting wilwood dynapro 4 piston calipers (these have dust boots and are ADR compliant) .. 300mm drilled and slotted rotors, braided lines.. brakes are totally fantastic !!!!!...

You can go up to a 15/16" hilux master cylinder, it just plugs right in. A little fiddling with the lines will let you plug a 1" landcruiser cylinder in. It's a complete non-issue when upgrading brakes on these cars! :p
 
Which brakes did you go with in the back? Gen 3's? I'm currently running stock adub fronts and the turbo rears and finally have something to use a prop valve for! :p