I suspect that your alternator is working ok, I am not sure why you are so worried about the rectifiers. If it hand cranks freely on open circuit and becomes stiff to turn with the dc leads shorted then it is most likely ok. If you have used new bridges and connected them correctly then I doubt that you have a rectifier problem. I was mentioning the " lumpy " turning more to question connection errors than a rectifier fault.
As wound that alternator will just about cut in at 200 rpm, it will give no significant power at that speed, you will need to get up to 300 rpm to get much out of it and if you have 40 psi at sufficient volume to feed 2 half inch nozzles you should be able to get a fair bit.
If your is turbine only doing 200 rpm then you will not see the tiny current on a 1000A Fluke meter. You could try looping the cable through the clamp 10 times and make it 100A FSD.
You have got a lot of confused ideas, the issue is not that the alternator will fry at 200 rpm, in fact it will produce so little that it won't really be on load.
The 200 rpm is cut in speed for the wind turbine, the operating speed at rated power will be nearer 400rpm and for hydro you will need to spin it at over 300 rpm to do much good. Wind works at variable speed, hydro is essentially fixed speed and you must wind your alternator so that the load on your turbine brings your turbine no load speed down to about 1/2 and this must be with the alternator producing an output power that matches the input power to the turbine.
Just disconnect the dc connection from the rectifier to the battery and the turbine will run up to its no load speed. This should be about double the speed when connected to the battery. If there is no speed increase when you open circuit it then the turbine is running on no load.
The issue about stator heating is nothing to do with low speed, the simple truth is that it will not stand a high continuous power out without over heating, you don't have a strong wind blowing on it to cool it and hydro power is constant without peaks and low periods for the stator to cool.
The design within its limitations is excellent for hydro but the power you can expect out is related to its operating speed. The slower you make the winding then the less power it will give without heating.
In fact the more I think about all this lot the more I wonder if you have gone the other way!. 40 psi on a small diameter Pelton may be aiming for a far higher operating speed than your alternator will match, in which case if you open circuit it and the speed shoots up to a very high speed ( in the 800rpm plus region) then it may be that you have dragged your turbine right down off its power curve and you have the opposite effect to the low speed issue.
Unless you give some details of the turbine then all this is total guesswork, I am now wondering if the turbine wasn't intended for a modified car alternator and intended to run in the 1000rpm region and you are loading it right down to about 250 rpm,
Flux