parasites can crash the system pretty hard, I was bedridden for a long time (or mildly functional) due to protozoa. These never showed up on conventional testing and finally got a lab that found them. Protozoa pull strongly on the body and will deplete the adrenals quickly.
Do you have any chills, fever, swelling or other noticeable changes (rash etc)?
There can be species that are considered commenseal but can be pathogenic. This is controversial. I would wait for the gut lab to come back and see if anything shows up.
The other thing you can do is to use a shotgun approach as mentioned in the post below.
The gut has 70% of the immune system and it is closely tied with everything else, so there is the possibility that the gut is reacting without being directly effected or second is that there is a gut pathogen.
I wonder what parasites are loaded in the PCR data bank that you tested with. If the parasite is not loaded in their bank then you will not get a positive.
Let me know if there is anything else I can help you with.