[J Smith]

Thanks Steve.
Before we started it up, we squirted some oil in the spark plugs holes and let it sit overnight. The next day we cranked it over by hand a few times to make sure everything was moving freely with no funny noises.
We got it started Sunday afternoon and it ran rough. Then let it sit last night and I adjusted the valves today to make sure they weren't out of spec. All were very close, and at the most some were only .001 off.
I'm assuming the problem has something to do with sitting for a few years.
I guess next up is a compression check. My brother is checking on some VW forums tonight to see if he can get any information as to what the problem might be.