SOLVED:
I was able to turn some very nice threads last night after figuring out the last of my issues. As I mentioned above the error between the two slots in my timing disc was the source of the inconsistent pitch issue. I suspect this particular problem was rather unique to my system since my index wheel rotates at exactly 1/2 the speed of the spindle. I have two slots on the disc so that my timing index still reflects a 1:1 ratio. Most people would have one slot because they are running the disc at the same speed as the spindle.
The problem with the pitch being wrong was also related to ratios. At first I thought maybe my Z axis calibration was wrong but it was spot on. In my pulley setup screen I had modified my pulley ratio to make the VFD and the RPM readout match. This was WRONG. The pulley ratio will reflect the ratio between the index signal and true spindle speed. I could have used this to keep just 1 slot on the disc with a 0.5:1 ratio, but instead I had the ratio set to 1.5:1. I only realized this error when it occured to me that the pitch I wanted was exactly 2/3rds of what I was actually cutting. Well, guess what 1/1.5 is? ) 0.667. When I changed my pulley ratio to 1:1 it cut a perfect 8tpi thread.
Since I changed the ratio on the pulley the VFD and the RPM readout were now significantly off. I fiddled with the rather miserable automatic spindle calibration function in Mach3 for an hour before I got the numbers somewhat close. They still are not the same (500rpm setting reads 460, 600rpm setting reads 600, 1300rpm setting reads 1100) but at this point I don't care much.