I have eco-complete in two of my tanks; my 45 gallon has eight skunk cories.
I had the same concerns that you do about the texture of the substrate and did a lot of reading before adding the cories. The general consensus I found from people who are both using eco-complete AND keeping cories is that they are fine with it.
The main question people have is whether it is too harsh for their barbels, but it seems that water quality is of more importance in that regard. Keep your water pristine and the cories should have no trouble foraging on the eco-complete. (Also, while the eco-complete looks like gravel, it does crumble fairly easily.)
I can't respond to your other questions about water parameters as there are too many variables in my tank to narrow any particular change to one cause.