John,
A little bit more precise way to be sure you are up on the compression stroke on #1 would be to take the valve cover off. Rotate the engine by hand, watching the rocker arms. When you see the #1 intake valve closing then start watching the steel ball and the pointer - when they are lined up you should be at TDC. Then follow Hotrod Lincoln's directions on setting the points.
If you had it running but it was very rough it could be that the timing is way retarded, the distributor is one tooth off or the plug wires could be out of order. To tell if it is simply out of time - while you have it running try moving the distributor very slowy to see if it smooths out. If it does, you can, for starters, time it by ear and find where it runs smooth but doesn't kick back when you try to start it (meaning you are too far advanced). If you can't turn the distributor far enough to get it to smooth out they you are either one tooth off on the distributor drive gear or the plug wires are not in the correct order.
If you are off by one tooth on the drive gear just pull the distributor out just far enough to move it one tooth ahead or back depending on if you feel it is too far retarded or advanced. Once you have slid it back in enough to engage the gear on the cam, you won't be lined up with the oil pump slot any longer. So leave the distributor where it is, install the hold down (with light pressure so it won't jump another tooth on the cam gear) and slowly rotate the engine by hand until the distributor shaft drops into the oil pump slot. Then add some tension to the dist hold down and start the timing process.
To check the plug wires, simple find which one goes to the #1 cylinder and then, going clockwise, the order should be 1-5-3-6-2-4,assuming it is the same as the later model 6's.
Hope that helps - I know that timing stuff can be frustrating. Good luck!
