woodsmith
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It would be good to let the joists dry out as much as possible while it's all exposed, at least the weather is on your side.
Difficult to tell water damage from a photo. Try sticking a thin screwdriver or knife into the wood, if it only goes in a short distance then the damage is superficial. You could also try tapping the wood with a hammer. Rotten wood sounds dull and you can see the damage the hammer does, sound wood has more of a ring and you should get no damage.
So if the wood is generally sound and the uneven top surface is the only problem I would get some 100 by 50mm timber and screw (use timber fixing or construction screws for this) or bolt this to the existing joists the full length of the joist. This will give a bit of support to the joists and a flat even surface on which to fit the floor.
Hope that helps.
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