Is this a serious conversion... like you're going to fabricate a top and do it right... or is this taking a junker and making it topless?
If its the first one, consider adding bracing across the bulkhead behind the rear seat, box the frame beteen the wheels (don't worry about front and rear), and put a triangular brace under the hood that ties in the upper shock mounts on the frame to where the cowl meets the firewall. The middle is just going to be floppy, no getting around it. You can maybe have luck adding another body mount or two under the doors to tie it into the frame more rigidly.
If its the second one, take out the body mount bushings and weld the body to the frame