That is the very same scenario I faced in 1989!
The bowls were missing on my car, both sides, both all rusted away, but replaced by OEM bowls.
The vertical inner sills were removed as the floor lip had gone in many places, both sides and these were Dansk replacements.
I made my own floor lengths with the same techniques as you, hammers and wood and a length of 25 25 x 3mm wall rolled tube.
The 'new' floor and the old were gas welded in as that was all I had, and an arc welder....
I hired a MIG and Spot welder as needed.
The Dansk outer sill had the same issue, the 'U' formed upper lip to locate to the inner sill was 8mm out and they needed a lot of brutal adjustment to fit.
I had the Dansk door skins to fit up to which were not the best reference shape.
The old sills that came off were from a Mk1 Cortina. Classy car my 911!
Still, you should try fitting a full sill set on an MGB, just as frustrating.
Barry (and others) make all this look simple, good tools, space (I too did mine in a single car garage/drive) and an Everest of skill and experience, but all is possible, just takes some time and thinking out.