Oh boy you have a good chore there don't you!? I have rebuilt several of these and would be happy to help you.
You are on the right track. You need to completely replace/rebuild the entire base to your cab-over. You need to remove the entire lower section of floor as you say. This is the whole part that sits above the cab from side to side and front to rear.
You can probably re-use the metal or fiberglass sheet that sits underneath so use caution when removing and handling.
You will want to use 5/8" or larger plywood to match the original thickness as close as possible. You will want to use old pieces for templates if possible and make new platform.
Attach the base metal/fiberglass panel to new wood platform with spray adhesive. Be careful because the glue will bond instantly when two parts touch together.
Use some bead board insulation or something similar to what you had and simply re-assemble everything in the reverse order of how you removed it. Go over the top interior portion with some new paneling to finish. Use long wood screws to attach the sides and front of the platform to the upper structure and be sure to seal up everything very well with new sealants.
Take pictures before removal to aid you in re-installation.
Take care and good luck, Steven