I have a potted papaya grown from seed that is about 8' (foot) tall.
I over wintered it in a heated conservatory (I'm in Zone 6a) and have it outside in the warmer months. This winter I must have over watered it since it developed root rot. I removed the plant from the pot and washed off loose soil and cut off the rotted roots and part of the trunk (about 50% of the roots) and then repotted in fresh potting mix and trimmed the foliage and place n a spot away from direct sun. I also watered with diluted hydrogen peroxide (didn't have any other fungicide on hand).
This was a couple of weeks ago. So far the plant is not looking too bad but not putting out new growth yet.
Generally the answer to major problems like that with these plants is to get a new plant or put in more seed because they grow so fast. But to save that tree you've done pretty well all you can do, except wait. I find once there's damage to the plant fungus gets in really easily. You could probably get some fungicide and water the roots and damaged trunk with a weak solution to give it more time to heal over.
Great job, growing one that big from seed, and also excellent job on the triage. I agree with tropicbreeze, you've done all you can do except once it starts a bit of new growth, get it out in the sun. Sun heals a lot of wounds. You could also try dusting any exposed cuts to the trunk with cinnamon. Can't hurt. It's anti-fungal and somewhat anti-bacterial, widely used for preventing fungal infection on orchids and the like. I buy it by the pound.
They're nice plants but you generally need more than one to cross-pollenate unless the fruit you got was from a self-fruitful variety. You'd be well advised to eat some more papaya and start some more seeds in any event. That big plant's most likely going to need some company of the opposite sex before you'll get fruit.