On the cart, they did all the panel alignment and gapping so I was debating installing my family cage while on the cart to brace it where I know it is perfect then shim it when I move it to my frame so the frame is shimmed to fit the body rather than vise-versa. Would you recommend transferring the body firs and starting over with panel alignment then install the cage?
Why do you think that the cart is "perfect?"
1. You want your tub on your frame with your mounts as soon as possible. And there shouldn't be a shim anywhere on an Early Bronco. (maybe between the hood and the cowl...but other than that, Bronco's don't come with shims.
@Wild horse 75 is giving you some great advice here.
2. There is no reason to build a Bronco and apply paint to it without performing appropriate surface preparation. That includes block sanding. I have never once heard anyone say that they wish they had spent less time getting their Bronco straight. Paint is an excellent magnifying glass. Every wave, or imperfection is amplified once you put shiny paint on it. It only takes a few more hours to get it right. If you don't block it, you will regret it. (and yeah, I've put countless hours of body work into my Bronco and my first camping trip I striped it with tree branches. But somehow it looks better to have trail damage over good body work.)
3. Who is telling you that you have to strip the body down to bare metal? NO ONE has sufficient intelligence or information to make such a claim. It is certain that a suitable surface can be achieved without removing the Chinese primer. I can also guarantee you that every painter will tell you something different. Fear, Uncertainty, and Doubt (FUD) is the basis for most automotive paint shop myths and legends. As soon as someone tells you that there is only one way to do something...it should set off red flags. There are always MANY best solutions. What normally happens is that someone will learn a method that works, and then they will promote it as if it were the only method that works. Then when you challenge them, it becomes: "Well, that's the method that works for me, and that's the only way that I will do it..." Arrogance and FUD is a very expensive combination.