I assume you have the floor boards and side sill plates in place. My advise to you would be to SOLIDLY bolt the body to the same frame you are going to use for the car. Align and if necessary shape the doors to fit the body openings and they open and close in a level fashion. Shim body to frame if necessary for alignment. Fit the rocker panel so there is about 1/8 to 1/4 gap from the bottom of door to top of rocker. Now you can make sure the cowl and quarter patch panels fit the body and the rocker when you fit them. To do all this alignment correctly is time consuming but otherwise the results can be disappointing.
Actually I like to do all the major metal fitting and welding, if required,while the body and frame are bolted together on 33s and 34s. Just have better fit results and less rework in the long run. Your results may vary.