Its been a few weeks since I've updated this post but here goes.
The main issue with the car was the secondary temp sensor and a bad thermostat.
It took me A LOT longer to do this swap due to inexperience and lack of specialty tools. It took me nearly 8 hours because I had to do it TWICE! :x If I had to do it again all over again it would probably take no more than 2 hours tops.
Here are some suggestions to make your experience much easier.
1) Make sure you have a nail laying around so that you can lock the belt tensioner in place.
2) I suggest buying a radiator clamp tool. t'll save you a lot of time and frustration! I bought this one from Sears http://www.sears.com/craftsman-cable...p-00947390000P
It's nice because it'll keep the clamp locked open as you position the clamp on the hoses.
3) Also pick up a radiator hose pick tool. It's easier to remove the hoses with this tool versus using a screw driver and brute force. http://www.sears.com/unknown-8-quot-...525209?prdNo=6
3) The MK II's have a secondary temp sensor that can only be replace by pulling the alternator. If you're swapping the thermostat, I would HIGHLY
recommend replacing the o-ring for the crossover pipe. I had to do my swap twice because I reused the OEM o-ring and it leaked coolant everywhere! I decided to go with a slightly larger o-ring to eliminate any possibility of leaks.
4) When reinstalling the alternator besure to thread the mounting bolts back in and tap them with a hammer to get the bushings to recess. If you try to reinstall the alternator as is you'll never get it back on.
5) Get a set of torx bits because nearly all of the little fasteners require them for removal.