Brian,
Thanks for the suggestion. It was actually shifting pretty well when the line was not hooked up. Several things that I noticed when I started trouble shooting the trans shifting. When checking the throttle linkage adjustment, I found that all the plastic sockets were cracked. I replaced them and did the adjustments per the manual. When chceking the travel to WOT, I found that the way the linkage was originally adjusted, the IP lever would not travel close to the stop. When I adjusted the linkage so that the IP lever would go to the stop, then it did not return all the way to neutral. That left the idle around 1000 rpm. I adjusted the idle down to around 550 rpm using the adjustment screw on the IP. However, it seems to run a lot rougher when cold than before. I am wondering if the pivot bracket that links the accelerator linkage to the IP is slightly bent, thus causing the limited travel.

Does anyone have experience with this bracket bending?

Last note is that I get around 11-12 second 0 - 60 mph times (have not been very precise with the test). So I think that most everything is working ok, I am just fustrated with the shifting.

Thanks