Are you getting O2 readings throughout the night? Lack of oxygen to muscles can cause them to ache later, I believe.
I've experienced lots of these, especially this hospital stay (and a couple of others). The fact it seems (admittedly, subjectively, since I haven't reliably checked) correlated to use of IV antibiotics, rather than severity of illness or other factors, makes me suspect I'm reacting to them, rather than infection in general. Is anyone on here using Meropenem, Amikacin, Tobramycin or Aztreonam?
Get something stronger than Ibuprofen if you need it. Better to face the (pretty minor, if well-managed) risk of addiction to, say, codeine than live in chronic, quality-of-life sapping pain. Insist on it being managed if the docs are giving you a workaround. I'd argue it's more the duty of a physician to help alleviate suffering than extending life, even.