Quite possibly flukes, the tend to look like gummy squares. Undigested fruit would not be solid, unless you are giving dehydrated hardened fruit, and digestion is so poor it comes out in a couple of hours. Trust your instincts, it's probably parasites......
Testing is useless....seriously I find it hard to believe it is recommended by long term users here....who they themselves have unresolved issues and a posting history of inconclusive or questionable test results.
The herbs may be a good place to start in addition to the foods you have incorportated, but it's very rare that they solve anyone's issues totally. I do know it's easiest to cleanse before big health issues arise!