I finally got to the point in my rebuild to set my timing but I a little confused on how to set this up.

The manual indicates that I have to rotate the engine until RT mark on rotor aligns with left hand pulse. Since I removed and reinstalled the rotor, I believe that the alignment may not be correct. Is there another way I could set up my timing, such as placing one of the pistons at top dead centre and going from there?

Hello, this might help http://gstwins.com/gsboard/index.php?topic=46805.0.
Check the NOTE on the image.

The rotor has a dowel pin to index itself with the crank shaft. Follow the manual. It shows how to do it, that is how I learned. Better to use the correct method, unless you want to risk bending a valve if it is wrong.

Thanks guys! All is good so far in the rebuild thanks to your information. Did a compression test and it seems to be within spec so I guess I did something right with the valves (ie no bending)].