My guess is low dissolved oxygen. The well water will only make the problem worse if you don't shoot it into the air or bounce it off of rocks, a packed column or something like that to get O2 into the well water. As it comes out of the ground it is virtually devoid of O2.
The trolling motor will help, but have the tip of the prop break the surface of the water to create splashing - putting more O2 into the water.
Same with the trash pump, splashing the water puts more O2 into it.
Google paddlewheel agitators or you could also use a surface agitator like this:
Volcano II
