I don't understand your statement about using the Ramcharger floor. You won't be doing that. You'll use the 54 floor.
Position your A-frame where you're going to do the swap. Move the Ramcharger inside the A-frame. Run 2 nylon straps through the front windows, one at the front of the window opening and one at the rear. Run 2 nylon straps through the rear windows, one at the front of the window opening and one at the rear. Now you have four nylon straps making four complete circles through the window openings and across the top of the vehicle. Remove all body mount bolts/nuts.
Get a piece of 2x3 or 2x4 steel tubing, long enough to go through all four loops with maybe two feet hanging out on each end past the loops. Drill a hole through the tube on the short sides (long sides vertical) and insert an eye bolt. Weld it, nut it or whatever. Slide the tube under the nylon loops. Attach your come-along to the A-frame and to the eye hook. Take up the slack and see if the car is balanced front to rear. If not, slide the tube forward or rearward to get the balance. Worst case, you may have to add some cylinder heads to the front or rear of the vehicle. Raise body off frame and roll frame outside. Back your flatbed trailer under the body and lower the body down onto the bed. Haul it to where you will store it or to the scrapper or to the guy who answered your craigslist ad for pristine Ramcharger sheetmetal.
Do the same thing with the 54, leaving the body hanging from the A-frame and rolling the frame outside. Roll the Ramcharger frame in and position it under the 54. Drop the body down and begin eyeballing where you will have to weld crossmembers and such to attach the Ramcharger frame to the 54 body, using the 54 body attaching holes. It sounds harder than it is. It's really a slam dunk once you get the 54 body hung over the Ramcharger frame. A little measuring and a little eyeballin' and you're there. Don't forget the four heavy duty jackstands under the frame on each corner. If the body drops while you're underneath, it could bottom the suspension and give you a headache.