Once you test out your wheel generator to see if it generates enough power at 3-4 mph (sailing speeds), and if it does work, I'm wondering if you made a bracket that mounts the unit just over and just in front of the rudder (so the rudder will still swing up). Then mount two paddle wheels (one on each side of the rudder). These would be 15 or 20 spokes coming from a 3 inch dia hub (not designed like that video with disks), I think the spokes with cupped ends would have less lateral resistance than a big old paddlewheel and be substantially lighter and less bulky (the spokes could be removed for storage). The paddle ends would only go into the water a few inches so when you beach you shouldn't need to remove them, the paddle generator system would stay on the boat all the time.
Check the wattage on the unit you have, if it's only a 3 watt generator, you might look into a larger 6 watt unit (only slightly more expensive), but that's your choice.
Your correct the unit you already have is probably waterproof enough that it shouldn't need to be mounted in a box if mounted way up there, the only thing it would see would be rain and an occasional splash, should be water proof enough for that. The spokes I would make from 1/4 aluminum rod threaded on the ends with lock nuts (so you can orientate the spoons/cups (perfect balance isn't important on such a low speed unit)). This unit itself should never need to be removed from the boat during your trip. The power from the unit I would route out with a waterproof wire with a waterproof plug on the end of the cord that would plug into your power station (Grid).
I still recommend you use a waterproof box as your control center so you can put your radios, cell phones, GoPro, etc inside the sealed box during charging (their most vulnerable time), leave enough room for 3-4 items, and wire in at least 3-4 usb plugs and wires inside the box. If you want to get fancy you can use lithium battery packs inside the unit (lighter), or just settle for a AGM 12 volt motorcycle battery (or something larger if you think you'll need it).
Even with the generator and the control center, I'm thinking if you get one or two of those foldable solar panels that you can lay out on the tramps, you can get additional power from those weather permitting, and also lay them on the ground when on shore near your camp site to keep you power center charged. Adding a few solar cells to the top of the box is also an option (every square inch counts).
Your control center would just bungy onto the rear storage area so it can be removed when you are camping and brought to shore to provide camp power. You will have charge controllers, plugs for USB power, 12 volt output (cigarette lighter plug), and an inverter for 110/220 power inside the unit (where everything stays dry).
If you have an unlimited budget you may want to look into adding an Evolve system to the mix. Your control center should be able to provide enough charging power to keep the evolve batteries charged up enough for occasional use. Basically you take along the charging unit that comes with your evolve system (stored inside your control unit and plugged in via your inverter to provide charging power for the evolve batteries ( I would take two batteries, use one battery, while the other is charging), also with evolve you may be able to charge and power at the same time (extending the battery range) just like the solar panel option that comes with the current evolve system does now but with your generator supplying that supplemental power vs the evolve solar panel (way cheaper). But that's all you choice and depends on your budget (Evolves are very expensive). The Evolve solar panel option is much more expensive than the more common 12 volt solar panel systems out there, I would set it up like I described above, verses the evolve solar options. Alternately you could design your entire system around the evolve 30volt battery systems (eliminating the 12 volt AGM battery), but I have a feeling it would be way more expensive.
Here is my take on sea adventure of long duration. You never know what to expect weather wise and you must be prepared with backup systems
for everything. And if you get caught out in raging seas and high winds (sudden storms) you have to have the means to get out. If your a mile out and an offshore 25mph+ wind kicks up your sail and mirage drives will not save you from being blown out to sea (this has happened to me more than once).
Also if the wind dies completely or becomes very unfavorable (head wind directly at you), or if your mast breaks, or your rudder breaks, etc, you have to have some means to overcome these possibilities.
Since your going on such a long trip I think if I were going on such an adventure I definitely recommend mounting a Honda 2.3 gas motor onto your TI as a safety backup (that's what I have on mine, and have actually had to use it on several dire occasions). The whole unit only weighs 27 lbs and tips up out of the way when you don't need to use it. If your mast or rudder breaks, or a storm blows in just power it up and get back to safe harbor. I have a trailer so the motor is permanently mounted to the boat (I have never removed it). Even if you do remove it, the motor is very light and compact. I've always had an emergency gas backup motor on my TI's for the last 3 1/2 years with way over 5000 sailing miles, just for my own piece of mind. Just stuff to think about when embarking on such a long adventure ( I'm only trying to help). I always carry 2 1/3 gallons on fuel on board which will get me between 150 and 250 miles.
Also you might also want to look into possibly powersailing your adventure boat exploiting the tri-power capabilities (wind, pedal, and supplemental power(hybrid gas/or solar electric)). If you go to this topic on my boat 'ultimate Tandem island' you can read up on some of the stuff that you might be able to use on long adventures (viewtopic.php?f=69&t=33720
), look into some of the later pages on the powersailing stuff). I found at least in the standard conditions we have in our area, if I want to travel any distance, I much prefer traveling at 6-9mph vs the standard 3-4 mph that a typical TI will do in low or no wind conditions. Plus when powersailing the actual wind direction is not a factor at all (you can sail almost directly into the wind if needed).
With your water generator idea you could pull the whole thing off with either gas supplemental power, or an evolve solar/electric system.
The main reason I'm responding to this at all is that water wheel generator may be the missing link in the chain needed for a workable solar/electric powersailing drive system to succeed, exploiting the tri-power capabilities of your Adventure boat (I've been working and thinking about that one for almost three years now). Once perfected I plan to enter the 300 mile Watertribe EC challenge with it (in class VI experimental electric), (http://www.watertribe.org
Just some ideas for you