OK, good, glad things in her throat are clear. Tyler it sounds to me like she could possibly have an infection or is developing one. When I hear these sounds from one of my birds I almost always start them on a course of antibiotics to either clear up what's there, or put a halt to what may be starting to develop.
The Cipro you have would be a first choice drug for respiratory ills in a pigeon (most times we would use what is called Baytril/Enrofloxacin, but Cipro is more or less the human equivalent of this). To treat her you would cut one of the Cipro tablets in half and put away one half. With the other half I want you to grind this up into as fine a powder as you can, here I use a shot-glass - like for measuring alcohol - and the end of a small kitchen knife that has a rounded end. When you have the pill all ground up, I want you to add 5mL of pancake syrup or honey to this, you can use the 1cc syringe 5 times to measure this amount, or you can use a cooking teaspoon (this is 5mL, but it must be a cooking teaspoon, not a regular teaspoon). I then want you to stir this very well, then let it sit 20 minutes, stir very well again and the medicine will be ready to use.
I want you to give your hen 0.10cc (this is to the first line on the 1cc syringe, and is about 2 drops, and will contain 5mg of Cipro) and do this every 12 hours for 7 days and we'll see how she is doing by then. Stir the medicine well each time you use it and keep it in the refrigerate between use.
Make sure she has seed and water and is kept warm and if you can tomorrow, I would not mind seeing you post up a photo of her and of her fresh droppings. Any questions, please ask.
Karyn