You shouldn’t have to remove the main body from the floor pan. These VW based CMC/Fiberfab kits had a “false” firewall, usually made of wood, accessible from inside the car. If you can remove that, you will probably be able to get at the rest of the bolts.
Good idea to replace the floor pans…you’re sitting on them.
Bummer that the seller was not “up-front”. Buying a used “regular” car is risky enough, now you know that buying 25 year old kits cars sight unseen is a no-no. As long as you have the cash, skills and time, you’ll get it corrected.