FishingRod,
I think that a combination of minnows would be better than either alone. In particular, the FHM begin reproducing earlier and the GAM reproduce in the hot weather when FHM stop spawning. So my sense is that the combination is better.
With regard to limitations, I think you are correct about #3 as being the primary limiting factor. Reproductive rates tell us a lot about how fast the limiting standing weight can be achieved. Yes, FHM and GAM though they are very resistant to low DO can have fish kills when they are not cropped.
On the final question, I would just say that I wouldn't use manures for fertilization in my water. Of all the available organics for fertilization, I like rice bran best but whether to use organics depends on what you are trying do and the existing status of mobilized nutrients in the water. Organic fertilization produces the best bang for production of fry.
