well i'm not too sure on the specifics of a manual swap on the mk4 but i would assume its similar to the mk3
rip out the auto.. bolt up either the 5sp (from a non turbo mk4) or the 5spd from a mk3 turbo (r154) or 6sp from the turbo mk4...
to make things easier on yourself find a mk4 with all manual parts in it
flywheel
driveshaft
clutch (or buy new)
diff
clutch master & slave cylinders
pedal box
that way your gearing is most likely going to be correct but you should really go and get it checked to make sure it's not out
you will also need to find out if your reverse lights are integrated into the neutral start switch of the auto... if it is you will need to rewire it or you won't have reverse lights (coz ur switch isn't there anymore)
good luck with it