check if the mk3 beam has a bias valve on it, if it dowes then it will swap right over, just fit MK2 gti rear discs to convert to 4x100 as said. if it doesnt have a bias valve then you need to fit one, either fit mk2/3 one after swapping over all the brackets required to mount it, or fit an manually adjustible one somewhere.
if the MK3 has 280mm front brakes then the calipers and carriers can be used on a MK2, just need 256/280mm front bearing carriers from a 4x100 car such as corrado, passat, SEAT ibiza/toledo/cordoba, high spec mk3 non-gti, MK2 16v/G60 etc.
basically anything SEAT/VW thats 4x100 with at lest 256mm brakes will work except polo/lupo and the SEAT equivalent (arosa?)