The potential problem I see with having to extend the firewall is getting rid of the taper in the floor. You're going to have to flatten it to move the pedals back, I think.
The problem I see with welding in boxes is that the masters needs to be a certain distance from the pedals. So if you move the pedals forward, the masters will be too long. You might be able to adjust the brake but the clutch would probably need to be moved forward as it uses all of it's throw. Now that I think about it, you would need to move the booster since the master is behind the booster and it would probably hit it if you moved it 3-4".
Lowering the seat would cause the same problem, I think. Lowering the seat will force him to extend his legs more.
Even if you had to redo the cage and shifter then pulling the steering column out a bit I think it would be more straight forward. Locate the proper seat placement then build the cage around it. Another idea is to go with a suspension seat. These use very little foam and no springs so they are a lot thinner. You could get 2" out of the seat and then only have to move it back another 2" to get you 4"