You might be able to cut out the damaged portions and weld or rivet in patch panels.
But if you need to do complete replacements of both sides of the pan, you are going to have to lift the body. The main body panels bolt to the original body mounting holes for the Beetle, which run along the outer channel of the floor pan.
My personal build experience is with Classic Roadsters Duchess, but I think all of the replica bodies attache pretty much the same way.
Former Owner of a 1981 Classic Roadsters Ltd. Duchess (VW)
2005 Intermeccanica Roadster
If you own a TDr and are not in the Registry, please go to https://tdreplica.com/forums/topic/mg-td-replica-registry/ and register (you need to copy and paste the link)