Sick Baby.... Please help

My son is 10 months old...

He has a really gnarly cough, runny nose, mucousy diarrhea, his cough/mucous is making him gag/choke, and his fever was about 99.4 until yesterday when it started being more around 100.

I took him to the doctor and she said "it a viral infection and it just needs to run its course".

Well since then he's started throwing up. It's currently 2 am and his temp is 101.1 and I tried giving him Tylenol and he puked all over the bed and himself twice. So I haven't been able to totally get his temp down (granted I took off his fleece PJs and that's helped a little) and I am terrified to go to sleep... I feel like I'm overreacting but I feel like something more is wrong. This is my first baby and the first time he's been sick. I don't know when to worry and when to just let it run its course...