Well I have just gone through a huge (to me) ordeal of getting my car running after doing a head and intake swap. So I figured I would write out some instructions to help the next person along, and honestly it can be very easy to understand, and I will try to lay it out as such.
1) Remove all spark plugs or just the #1 cylinder one. (Removing all makes it a lot easier to turn over by hand).
2) Place your thumb over the spark plug hole, and turn the engine by rachet. As you turn you will eventually feel pressure pushing your finger out, at this point you have found the compression stroke of the engine.
3)Now once you determined your on the compression stroke, look at the balancer. It should be close to the 0 mark (TDC), turn the engine so that the timing pointer is at the 0 mark. (If you installed a cam, I would have to assume you ensured that when you put the balancer back on, it was correctly done, where as the 0 mark on the balancer is in sync with TDC of Cylinder #1.)
4) Now, drop in the distributor, keeping attention to the position of the TFI module.
5) Once you have dropped it in, put the cap back on and identify where the #1 spark plug terminal is. (It maybe easier to do this prior to dropping it in, but no difference.)
6) Now turn the distributor so that the line and the rotor are centered in each other. (See pic below) At this point, the car timing is set as 0, where as the spark will fire as the cylinder is at TDC. However we want it to fire before it reaches TDC, so we will need to turn it slightly clockwise to advance it.
To get it right you should fire the car up, and then immediatly check the timing with a light.
The position of the rotor when its dropped in is not overly important, you do need it to be be point towards the rear of the car since the TFI module is on the front, and the cap only fits on one way, and the #1 terminal is towards the rear. You just need to make sure that you have enough travel in the distributor so that 1) you can line up the rotor with the line you drew on the cap, and 2) you can then turn the distributor clockwise to advance the timing. Often if you are not in the right spot, the TFI module will hit and you will not be able to advance the timing as far as you wish.