A fever is actually a good sign - the body's defenses are trying to work against the infection. Don't medicate it too much - let the body work. If he's miserable with aches and pains, then give something for that which will also reduce the fever.
Try lukewarm baths/showers - he'll hate it but it can bring down the body temp. The spitting up doesn't surprise me at all. There is probably a lot of postnasal drip, and that works its way into the stomach. If it's from coughing, then it's the congestion in the bronchial tubes and the lungs. If the test results are negative for strep, then they will tell you "it's viral" which means they don't know and can't do anything. My son had a vicious case of mono a few years ago, bad enough that it showed up on the first blood test. (A lot of cases don't show up on the basic office test but will on a second test.) But even so, it's viral.
My son was a healthy kid, strong athlete, and then was completely flattened by this mono - in fact, his spleen was so enlarged that we could see it protruding from his chest and the doctor told him not to wear a seatbelt in the car! His throat was so sore from coughing and the rest of the infection that he wasn't able to eat much, and then he declined further. The throat was so sore it was bleeding. Still, we were told to just push fluids and let him sleep and watch TV. Fortunately, his coach (and the head of phys. ed. and wellness for the school) told us about nutritional products that support hydration and immune system strengthening. Turned our kid around in just a few days. And we've all continued that nutrition since, with remarkable results. Your son's situation is probably complicated by the allergies which create a whole bunch of swelling and phlegm and drip and so on. I had those as well, and it always made my bronchitis worse. So things overlap.
So I'm saying not to panic, and that even if it is mono and some of the symptoms he doesn't have now do occur, there is plenty you can do about it that won't conflict with any medication he might be given. Mono, for example, has a whole bunch of possible symptoms, but not everyone has all of them at the same time. We had tons of allergy and upper respiratory problems for years (I had them my whole life) but were able to turn it around.
Since then I have trained and now work extensively with immune system issues, and I have seen a zillion cases like your son. It's normal to think, "Oh this is a healthy kid and he's been affected now by some horrible debilitating lurking illness that must be serious and they just aren't telling me or testing for it." More likely, he's been building towards this for a long time and it's the same thing pretty much everyone in the country has - reduced immunity! It can be addressed and I'd be happy to help you, but I think you don't need to panic. The question is, how long will it take his body to fight this on its own, and how long do you want to wait it out?