If they came out OK, it sounds like the bulkhead has moved. The bolts are the main support for the bulkhead although the wings and footwell supports should hold it roughly in place assuming they are in OK condition.
Is the bulkhead hole lower than the outrigger? If so, try sticking a jack under the bulkhead.
Do your doors still line up the same? Again, if the bulkhead has moved, they will not open and close well.... if they ever did on a Defender!