You need to add some shims under the rocker stands.  You mught need to go to a longer rocker arm stud.  Many VW performance shops carry them.  Look in VW mags for a place.  One is www.cbperformance.com (shopping with them for over 15 years and no problems...)

You can also go to cut to fit push rods and make them shorter than the stock length.

This is no big problem but is common when the heads are flycut, add some shims and you are good to go...

Robert