Hey Andrew,
Welding new steel over the rot was something we thought about at first since it is obviously much easier to do. It would also be stronger with the double skin, but only at first. Mud and water would get trapped between them and it'd be like termites for steel. You wouldn't know there was a new rot problem until the newer upper layer began to come apart.
Certainly better to go ahead and cut the cancer out while you are tearing everything else down. That way it will outlast you and someone else can enjoy it while you're pushing up daisies for them to drive on
On that small tranny output gear, I know that Rod Shaver had them NOS a couple of years ago. Sure he still has some available. If he still isn't responding to messages, it could be he is not currently on-line. The MVPA national convention in the USA was the week before the W&P show in the UK and he likely attended both events and may not be home.
If you ever make contact with him, ask him if he still has Windsor carbs. They have a different part number from the T-16 type but we determined the only difference is the choke mechanism. T-16 is set up for an electric pattern and the Windsor used a manual style. Internal parts and most of the cases are the same so its a viable source for NOS spare parts if needed.