I've been taking doxazosin for 3 months and I have noticed that my kidneys or sides have been sore?

Back pain is a common side effect of doxazosin, but if your pain is localized to the sides and close to the kidneys then please see your doctor.

Other known side effects are stated below:

Check with your doctor if any of these most COMMON side effects persist or become bothersome when using Doxazosin:

Back pain; diarrhea; dizziness; drowsiness; dry mouth; feeling of a whirling motion; flu-like symptoms; headache; indigestion; lightheadedness; nasal congestion; nausea; pain; stomach pain; swelling; tiredness.

Seek medical attention right away if any of these SEVERE side effects occur when using Doxazosin:

Severe allergic reactions (rash; hives; itching; difficulty breathing; tightness in the chest; swelling of the mouth, face, lips, or tongue); blurred vision; chest pain; fainting; painful and prolonged penile erection; pounding in the chest; puffiness in hands or feet; swelling of eyelids.

http://www.drugs.com/sfx/doxazosin-side-effects.html