So 5rpm in the creek will give me 50 rpm on the intermediate shaft which will produce 500 rpm on the generator (or so the theory goes)
This would be 100:1 speed increase. Sounds like it is going to need a LOT of Torque to just to overcome the gearing drag let alone power anything on the final output.
I was putting together a Post hole Differ this afternoon that has a 40:1 Reduction gearbox on it. Just twisting the output shaft to make the input side spin up, Even with a Screwdriver as a lever took a lot of effort. I think for 100:1 gear up, you'd want to be using serious shafts and gears because even if you do have the torque, once a resistance is applied at the other end, the forces on the Primary drive components are going to be Huge.
Going to be 100X speed magnification and even more Torque multiplication.
It would seem to me that there is only so much driving power anyway and the the least path of resistance will simply be around the waterwheel rather than through it.
I played around with F&P motors a while back and I would say they are a pretty " savage" sort of a generator. They don't need much speed as they come out of a washer to generate high voltage (gave a few friends some good belts after I did it to myself and realised how ppowerful they were) but the torque is going to be reasonable to get any power out of them. Even spinning them with no load creates some reasonable drag, maybe just from the fields energizing.
I have nothing but mucking around and gut feeling to go on but I would think that given the power I imagne you have from the stream, you would probably be OK at 100 RPM on one of those motors to make power which would be at least a couple of hundred volts and then pull it down to what you want ( if it's for battery charging ) from there. If you want AC, My gut feeling is you are not going to get much more than to light up an LED globe, If that.
Not trying to put you off, more like noting my predictions to see how far wrong I am when you get the thing working. :0)
That said, 100:1 gear up still sounds like a lot of parasitic drag to me.