Ok so I am doing the whole collect your stool samples for the next five days so they can check for everything under the sun. I have however been gluten-free for a while, will that change the results?

What are they testing for? Gluten consumption has nothing to do with tests for other things. Only if you were having bloodtests or biopsy for Celiac would you need to be worried about having been off gluten.

EDIT: I'm assuming your being tested for parasites, bacteria, etc.?? That has nothing to do with whether or not you're eating gluten.