Ken,
Every body kit comes from MD Juan regardless of who is selling it. Every body that has been made has been off. Even the "newer" revised bodies still need tweaking.
The absolute first thing I would do is let KW know where it hits and how much gap there is between the "outriggers" on the frame and the hat channels where you mount and the fact that the fenders won't line up either.
You will have some options like getting bigger spacers to get the body to sit up higher so the transmission won't make contact (then you'd need to create a fix for the other parts that sit up higher), or cut the center out and weld a patch in to allow the hump to sit higher. The spacers (or liners from the Parts Manual) were originally almost all at 1/8" (thin) or in some spots 3/16" (thick).
There are several "how to's" on the 3B Page, the 2A forum and I suspect here too. They will show how modifications need to be done. What's important is clearance (as you've seen) and alignment - where the holes line up.
