Seriously though - sounds like a pretty impressive expedition you have got planned there and I think if you do some digging around you might find reference to another Hobie MD Kayaking expedition that was being planned all the way down the Mississippi [sic].
You'll have to get pretty fit I would have thought - but joint endurance may be as much an issue as leg strength/endurance - in my experience there's a lot of stress on knees when you pedal day in-day out, but you do not get the same kind of 'stressed-muscle' exhaustion in a Hobie MD kayak as you would if you were walking, running or even cycling (because there's less impact than walking & running and you can't 'overdo' the pedaling like you can on a bike). I am getting older and more injury-prone and these days have a policy of taking anti-inflammatory meds (specifically: ibuprofen) with me on my madcap trips - seems to help with the overnight recovery and can also be taken on-the-go as long as you follow dosage rules.
If you are going to carry all your gear for the trip I would go ultra-lightweight - there's not a whole lot of stowage space on these boats and you really don't want to be pedalling more load than you have to.
Also be aware of the serviceability of your drive(s) - over that distance you can expect failures in fin masts, cables (plus their nyloc nuts in case you drop one overboard), pedals so you absolutely must take spares and tools (you will need small spanner, pliers, and the right size allen key for the pedal spring-lock assembly) to replace breakages in those components.
In my experience the older drives are more easily serviced 'at sea' w.r.t. a broken fin-mast (the commonest failure in my experience - though only on turbo fins which I assume is what you would use) at the expense of being a bit heavier and more clunky, so I retro-fitted the older cotter-pin style of fin masts to my newer drives just to improve my ability to be completely self-reliant in the event of a fin-mast failure when far out at sea.
Personally I would attempt the trip in a downstream direction
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