I've got floor shift and a straight six in my '64. So....
I'd think the shorties would simplify matters a bunch. I had to remove the z-Bar, install the full length headers, then re-install the z-bar. That was a pain in the lower back! The z-bar goes between the rear half header tubes on the six. (Hedman)
With the shorties you shouldn't have to deal with that indignity. I'm not sure that any long tube headers will fit with your configuration. But, I didn't look.
Call Hedman or your favorite header company. They should be able to answer your question.
CJ