Your new frame requires shimming from scratch, so the fact that you did not save the shims by mount position is moot.
Proper alignment may well take the best part of a weekend, and you will be good and sore after this exercise. First, put the body down on the frame with the proper cushions, spacers and washers in place, and be sure all bolt holes and hardware are centered over each mount hole. You can shake the body into place if it has been stripped clean, as it only weighs about 300 lbs. and this should not take too long.
Next thing is to get the radiator support loosley in place and attached to the inner fenders and frame (without the radiator in place). In some models, like my 64 roadster, which is not all that different from a C-3, the #1 mounts at the windshield pillar do not have frame/body cushions (cushions are on top), so this would be the reference point for all the rest to start with. Use your assembly manual for the actual configuration, as each year seems to have it's differences. Another good resource for parts identification is Dr. Rebuild's catalog.
After seeing how the body fits without shims, check the door and jamb gaps and alignments (assuming you did not remove the doors from the hinges, these should still line up) and see if there is any space between cushions and body frame on #2, #3 and #4. Fill these in with shims - use the old ones after sandblasting and painting. After filling in these spaces, slightly jack the body up using a 2x4 to distribute the load starting at the #2 mount - alternating sides - to get a constant gap at the door jambs. You may have to remove a shim from the #4 mount to get correct alignment. Repeat this process untill all door gaps are even, and all shim voids are filled. The mount bolts should be tightened snuggly to adequately compress the cushions for all alignments. After the body mounts #1, 2, 3 and 4 are perfect, then put the hood on and verify what shimming of the radiator support is required to even things out in the front. Some mis-gaps at the door hinge can be taken up with the radiator shims. Install any inner mounts and shims (next to the tunnel) after everything else is torqued down.
The whole process is just one of lots of common sense, and you will be surprised how a simple 1/16-inch shim can close or refine a 1/4-inch gap! The key thing is to not put undue stress on the fiberglass, and let the shims "do the work". Be sure not to forget the shims between inner fenders and radiator support.
Lots of luck.
Jack
