I'm sorry that your question wasn't answered in a timely manner. We don't have many avian vets on this site. Regretfully, fluffing and lethargy can indicate any number of illnesses or health issues in chickens. In avian medicine, there's rarely one cause of such a presentation, so we usually begin with a list of differential diagnoses and use lab tests, X-rays, and physical exams to differentiate one from another. Necropsy of a newly dead or a sacrificed severely ill bird then refrigerated (not frozen) can be an important diagnostic particularly in large production flocks. If you have such a flock, your best course of action may be to have your county extension poultry service or avian vet (please see here: www.aav.org) arrange a necropsy. I understand that this may not be appropriate for a pet chicken, however.
As more and more backyard flocks arise, the demand for veterinary care has similarly increased but little in the way of over the counter drugs exist for their care and so flock owners are quite handicapped in how they can help their birds without the aid of a veterinarian; however, it's best to approach the diagnostic process with a clear sense of her financial value to your operation. Although some services such as your county animal disease diagnostic laboratory might be available free of charge through a county agency or land-grant extension office, the expense of some diagnostic tests and treatments can add up quickly. While it’s always worth your time and money to identify a bacterial or viral infection that could potentially impact more than one member of the flock, this might not be the case with a condition that only affects one hen. It frustrates me that I can't be more specific for you but such is the dilemma of poultry owners and vets alike.
To answer you directly, rough shelled eggs are seen with diseases such as infectious bronchitis (IB), paromyxovirus, avian influenza, and egg drop syndrome (EDS) but there are quite a few considerations for shell quality as you can read here: http://www.thepoultrysite.com/articles/1003/factors-influencing-shell-quality/
Please respond with further questions or concerns if you wish.