Actually, the problem is that the S1 headlights and the S2 headlights are actually wired slightly differently.
Basically, Mk2s have the headlight wiring different than the mk1.
EASIEST WAY TO FIX THIS:
Look at your S1's headlight wiring, and note where the colors are (on the ouside and inside headlight beams)
Look at the S2's headlight wiring. Use tiny screwdriver to disengage the terminal clips and switch the wires to match what the S1 had them like.
Allow me to offer one more suggestion:
RELAY YOUR HEADLIGHTS!
Since you have to re-route your wires anyway, it just makes sense.
Timbo's how to:
You will only end up using the low beam and high beam trigger wires and running new power and grounds.
Also, get some Euro H4s. They are amazing!
H4 outer headlights with city light:
H1 inner headlights:
2010 Sportwagen TDI
I hate to nit, but relaying isn't just for upgrades. Sure, the added illumination you get when you are running straight power from the battery to the lights is nice, but I feel the more important issue that you correct with relays is preventing your stock switch from melting/catching on fire. It has happened many times, especially with those running H4/H1 bulbs- even happened to me in my Mk1!!!
Ok, getting off my soapbox now.
'81 Scirocco 'S ...
'05 New Beetle TDI
'02 Jetta Wagon 1.8t, tiptragic to manual swap.
'76 Kawasaki KZ400
If the issue is just to keep the switch from catching fire, wouldn't it be much simpler to run one new power power from the battery to under the dash and wire 2 relays (high and low) to the headlight switch? I wouldn't relay my headlights in the way mentioned just because how much of a mess it makes.
Or you could do what I do, leave the stock wiring in place, tucked away for use as a back up if need be, then I just run leads from the drivers side connecter to the relays, which I have 3 of... One for the low beams, then one for the outer light high beams, and one for the inner driving lights
Oh, and I run Hella Optilux 80/100w H4's, and Hella 130w H3's which I got from rallylights.com