I don't see any merit in removing the inner wings because some spot welds might have split. Getting them off is likely to stretch or tear them, and painting inside the chassis legs and then welding is a waste of time as the heat will burn the paint off anyway.

I'd redo the welds, either spot or seam is your choice, then get loads of rust inhibitor into the chassis rails till it drips out.

For the tunnel, you will see two seams that go across the car, one just in front of the centre crossmember and the other about 6" in from the bulkhead.

I opened those and fitted my 4x4 tunnel in the same place, with overlapping joints running fore and aft in one of the pressed indentations.