well if you latch is working then something is off. how is the fitment of your front quarter panels? Go over all the panels you put on making sure everything looks right. Also make sure nothing is in the way of the hood going down all the way. Also check the gaps between your side of your hood and the fenders there should be that 1/2 gap all the way down if not then the panels are on incorrectly
I have never swapped out front ends but I don't think anything was different on the latch assemblies throughout the years with mk4's but someone may know something I don't. But I would measure and take a look at your old hood just to be safe. Otherwise try raising the latch assembly a little more and that may do it
Also take those eyelids out it just ruins it.
Modified by ruetzal at 11:14 AM 10-14-2009