Allergies or URTI?

I was looking at the questions on cats, but couldn't find one that was close to what I'm seeing.

I'm fairly sure that Arizona has pollen or dust allergies, but not entirely. Here in the past three weeks, she has developed a runny nose that occasionally just drips a drop or two of clear, watery fluid. She isn't sneezing or wheezing, but today one of her eyes overflowed with the light-brown watery fluid, as well. I wiped it up with a soft cloth, and haven't seen another overflow today. She is also shaking her head somewhat regularly - about once every quarter hour or so when she's not asleep. It sprays tiny droplets of fluid everywhere. Her eyes are not red or swollen, and her ears are not hot, swollen, or dirty, and they smell normal. She is having a bit of stinky gas, and her poo was lighter colored, larger, and softer than usual - it normally doesn't stink, but smells awful today. It wasn't runny, just kindof poofy-looking compared to the usual compact, nearly-black links.

She does not get vaccines any more; her last vaccination visit ended with an emergency vet visit because she had gone into shock and was having severe difficulty breathing. She is known to have food allergies to corn, wheat, and rice; she is also sensitive to beef, goat, lamb, and bison (she will hork them up about 15 minutes after eating, even if she hasn't had them in months). She is eating, although lightly. If it is likely to be allergies, what would you suggest doing? My vet has suggested half a tablet of Benadryl for when she gets the red, itchy eyes - but her eyes aren't showing the usual allergic symptoms I'm used to.

So, I guess the root question I have is: How do you tell the difference between cat allergy symptoms and some sort of respiratory infection?

If you answer this directly, thank you! If not, it would be interesting to see a blog post about how to tell the differences. There isn't a really good article or whatever on Google or Ask. Thanks again!