In English, we would not say "my body doesn't feel well". As a general statement we would say, "I am not feeling well." Or "I don't feel well." Using the word "body" in the English sentence is making the mistake of translating each word in the Chinese sentence.
Since the Chinese phrase sounds equally awkward I just went with an awkward-sounding literal English translation as well. Some variation of "我不舒服" or "我身体不舒服" might be an improvement...