The easiest route is to use the PB head, because it means everything just bolts up and you can use the same management etc.
If, as I seem to recall the ratios are shorter in the GTI box then performance will be sparkier with the it, rather than the one fitted to the 2E, which will give better economy, but will blunt performance, rather.
This is why people sometimes fit the fifth gear from the diesel box - interstaller fifth for motorways.
I'd go 4-branch over OEM manifold.... although I'd want a 4-branch with long secondaries to pull the torque out of the motor, some some short-changed bunch of short tubes.