Body aches are the worst part of an active infection for me. My O2 stays high and SOB is controllable when I have my usual infections. But the aches are bad and often the first thing I feel (in my right hand, specifically)--well, that and yucky tasting, increased cough.
If my infection/inflammation markers are higher (elevated ESR and C-reactive protein) then I ache. Sometimes, but not always, I get a lighter version of this feeling before my period too.
It is different from how I feel when my muscles are sore from dancing or when I feel itchy/achey after my allergy shot. Muscle soreness does not make me want to lie on the floor and cry... (It actually gives me a bit of a high lol.)
Fighting lung infections is a systemic activity for your body, and it can make your whole body feel awful. Some people are more prone to aches/joint pain. Traditional arthritis is when your immune system attacks the joints. People with a positive RA factor are more likely to develop arthritis. But people without it do too--probably when their immune systems have received so much stimulation from constant lung infection.
So, the aches are most likely because of elevated inflammation in your body. This can be determined with blood tests.
(For someone with non-CF bronchiectasis, they typically check antibodies to yourself--RA, ANA, Sjogrens, Sarcoidosis--since it is not a chloride channel problem causing the over-production of mucus/inflammation.
Tangential joint and lung stuff:
I mentioned this once on this board before. I read a while back that anthropologists believe that fighting off TB is linked to RA (looking at skeletons from long ago, trying to determine if RA was in the Americas prior to European presence...it was). The hypothesis being that people who successfully kicked a TB infection had over-aggressive immune systems. The thing is...some infections, like TB, can be in your bones too, so perhaps RA starts with an immune system activation there...that does not shut off.