yeah i believe you do take the pulley off to re clock it. your re-clocking the front part of the alt case ( the mounting bolt holes).
as for the pulley, i used the old 2g alt pulley...
however......you may notice on the 3g pulley there's a bit more of a shoulder behind the pulley than there is on the 2 g pulley. i used a very thin washer/shim to put the pulley out to the proper depth.....you may or may not need to do this depending on how your pulley alignment is, which is something you need to check regardless...
the stock 2g pulley on mine with out the washer put the pulley a little to far back.....it may or may not on yours. it's no biggie, easy fix, but regardless of which pulley you use it's a good idea to dry fit the alt and make sure the pulleys line up ok.
you can probably use the 3g pulley, it wont drive it as fast as the 2g one, but you may not need it being driven faster depending on how it acts at idle with everything running....and as hissin suggested, u/d pulleys may also dictate which pulley you would want to run...