Your shiners are breeding right now and more than likely that is why you are seeing some dead ones. Their bodies get extremely soft during breeding and makes them more susceptible to just about any stress. So it is not unusual to loose some.

As far as structure I like to see people use wooden pallets stacked four or five high or even cedar trees. SW Indiana is know for these. They make great structure. 75% of your structure should be in water no deeper than 6 ft.
I hope this helps.....
Oh one last thing, if you are spraying rip rap, then use Aqua Pro or Rodeo they are much safer.

"Don't believe everything you read on the internet!"