Lymph nodes swell when the body is trying to fight something off - part of the immune system. If your son has a compromised immune system, the lymph nodes are swelling and the lymphatic system is trying to do its job, but is not being successful. That's probably why you are seeing fever and an increased number of swollen nodes - he's trying to fight off something (could be anything) but just can't handle it.
Suppressed immune systems are becoming more and more common - that's why we see "adult" diseases of all sorts in our children.
I would try not to have him sleep with you unless he really needs the comfort - the sweating is a big excessive and the close quarters may be a big part of this.
I've had this before, and it was nothing. But other people have it and it's a sign of a larger problem. I think the fact that they aren't getting anywhere in 6 months is a big clue that you aren't doing the right thing with the right people. (not a critique of you - just of "the system").
I do think you should consult a pediatric specialist and have those other nodes checked. If everything is still negative, you can look into immune system support (a nutritional approach, not a medical one). You can do both at the same time. My son had severe mono and did test positive - did the doctor tell you that a lot of mono tests come out negative anyway? Did they test in the office or did they do the 2nd test in the lab? I know mono is less common in very young kids, but so are many other conditions that didn't use to hit kids. But the point is, it's viral. Same as flu (all strains). Strep of course is bacterial and responds to antibiotics. Is your son's spleen normal size or is there enlargement? (My son's spleen was severely enlarged, to the point that they didn't want him to were a seatbelt - I know, like when does that ever happen? He responded to nutritional supplementation very quickly.
I hope you find out what you need to!