Thanks everyone for the input and suggestions.
I was able to adjust the max return settings to 50,000 and while it does slow the app down a bit, it is not intolerable. I did figure out that above 90,000 results the app returns a stack error.
I did speak with an ESRI Programmer at the UC recently, and I have supplied him with the query and my data. He will be looking in to the filter results returning data from fields other than what the query is based on.
I will post results as they come in!!