my son has a fever and complains that his penis and stomach hurts?

[SDaniels]

2 weeks ago i took my son who's almost 3 into the doctor for a fever and cough runny nose all the normal viral stuff. the doctor told me he felt it was viral. i also told him that he has complained about his penis hurting and his stomach hurting. he said if the fever came back then to bring him in. so here we are 2 weeks later and friday night he had a temp of 102 then during the day saturday had a temp of 100.7 then at 4 am this morning he had a temp of 102.9 the advice nurse said take him to the ER because of his stomach pain and he was so hot it almost hurt to touch him. the doctor in the ER tested for strep negative they couldn't get a urine sample from him but they say a bladder infection in a 2 yr old boy is rare but can happen. she pressed on his stomach to see if maybe his stomach hurt on the right side and no reaction from him. so here we are sunday afternoon and his temp will climb in the matter of 30 min. is this normal and does anyone know what i might be wrong with him and does appendicitis start out mild in some cases and get worse? any help would be great. we are working on potty training but it's not going to well.