As a layman it seems far easier to repair existing damage using nanomachine than to replace organs.

Not really. We have organ-growing capability, we don't have organ repair capability. It's easier to repurpose the former than invent the latter.

im not a biologist (anyone qualified to comment please do) but i dont think the new organs will stop the free-radical leakage. it occurs in every cell in your body, organs are only a small portion of those cells.