Here is an update. Got back from Sedona about an hour ago and cut the bar to 56 1/4" and it fits perfect. The bulb gasket fits flush, and the bar fits in the track just as it should nice and snug. I can tell this is going to fit my needs perfectly.
I will give a small review for the Bestop after using it for the first time today. I started off trip driving roughly 60miles up north to Sedona with my 2 dogs in the bed. The side windows were on and the back was rolled up, and despite heavy cross winds the top did just fine, and the dogs didnt mind one bit.
When I got to Sedona I had someone stop with me at a gas station so they could get the manufacture of the top so they could order one for their taco as well.
I then zipped the sides off and stored them in the back seat. Driving at speeds up to 60mph with the sides off and the back rolled up there was no problems. The dogs spent almost 3hrs total driving time, and about 45min when we went into a restaurant to eat, and didn't phase them at all. BTW the dogs are a German Shepard, and a Great Dane.
All in all I am very impressed with this shell. Despite the one hiccup with the tailgate bar install was very straight forward, and easy. The directions could have been a touch better, and now that I think of it I should have done a write up while installing. Thanks for the help, and hopefully this thread will help someone else.
New right side
New left side