If it tastes good, it pretty much can't have "gone bad." Cider has a naturally low pH, even before fermentation, and that combined with the alcohol makes it inhospitable for pathogens. Fermentation has been shown to achieve "five-nines" (99.999%) destruction of E. coli in apple juice, for example. So, rest easy on that one - you aren't getting a nasty bug from your cider. (When cider does go bad, it usually becomes vinegar, which is still good for you!)
However, it is still possible that it is causing your intestinal problem. Antibiotics take out the good and the bad alike, so your gut is defenceless against things that normally would not bother you at all. Yeast, for example - normally they have to compete with the bacteria in your gut, but now they can proliferate if you also eat something sugary. You can also have a problem digesting things that are normally broken down by gut flora, so foods you would ordinarily eat without any trouble will cause cramping and gassiness because the right bacteria are not there to help.
I'm not sure what it is in cider that gives some people gas, but it is a well-documented phenomenon. Perry is much worse, and the culprit there is sorbitol, a refractory sugar.
But none of those things should have given you chills and aches. You probably should go ask your doctor about that. There is a significant risk of opportunistic infections after surgery, especially after a strong dose of antibiotics. (This is how people get C-diff, which can kill you.)