Well, I may get the bad mom award, but... I don't really go by the number on the thermometer in determining when to call/take them in. I go more by how they are acting: eating, drinking (or not), acting lethargic, are they sleeping a ton, etc. Esp. with a newborn, if you can't get her to wake up and eat at least 5 or 6 times in 24 hrs., I would take her to the dr., because they can get dehydrated so quickly. Once that happens, it is way more traumatic for them, and harder for them to bounce back. IMO, it is better to call and get the dr.'s opinion (or the nurse, however it works in your office) about it, then to wish you had, kwim? Maybe you feel like an unprepared, paranoid first-time mom, but that is why they are there, to help walk you through these times. Again, go with your gut instinct: you are her mama, and even if you don't think you know what to do, chances are your first reaction is correct.
As far as medicating a fever, I rarely do, simply because fevers are therapeutic. However, my rule of thumb is if the child is too miserable to sleep comfortably at night, I will give them medication. Sometimes a half dose (or two half doses a couple of hours apart) is enough to make them comfortable. Trust yourself, if baby is so miserable that she can't nurse, she needs some help, and that is why the medication is there.
Here are a couple of other things that have helped my babies when they are congested:
Prop them at an angle, like in the car seat, swing, bouncy seat, on your chest, etc. It helps keep the fluid moving down, which is also good for preventing ear infections.
Steam baths/showers may loosen the mucous and make it easier for her to move it out as well.
Small amounts of a eucalyptus rub (like vicks or something comparable from the natural foods store) on the feet improve their ability to breathe. I usually do that before bed, and put socks on the feet to keep the rub there. Just a small amount is effective; don't overdo it, because a strong menthol (like in their noses, so don't put it on your newborn's chest) can make it difficult for them to breathe. I haven't found that to be a problem with older babies (like toddlers).
You are a good mama! Hang in there, it is hard to see your baby so uncomfortable, but you will both get through it just fine.