Finally get to pretend I am one of the cool kids - Holley kit swap
Here is my solution to getting the plates on the wrong side on the lower crossmember:
There are now half tabs that help to locate the parts side to side and if the parts are on the wrong side they won't allow the parts to nest. I also added a triangle to all the DS ends of the parts except for the inner skin of the upper crossmember.
Assuming the bottom of the lower crossmember isn't broke backwards, it should make it fairly easy to get it all in the correct orientation.