I just finished replacing the water pump, head gasket, serp+V-belts on my '96 Jetta GL, ABA engine. Now it is running rough. I have checked timing twice and all required timing marks are lined up. Could this be a spark or fuel problem. I am going hook up a scan tool soon but I though I would check on here in the mean while. What is the problem?

Check each of your spark plugs for signs of rust or any indication of water in the cylinders. Also look for any differences. Sometimes water can leak into the cylinder during the down stroke after changing a head gasket. Have you done the final torque down yet. Check your ignition - spark plug cables... and make sure the gap didn't get messed up on any of the plugs while you had things apart.
The timing would still be the most obvious possibility and I doubt it's a fuel issue.