the microorganisms that eat the rotting fruit are the same that eat the manure, organisms such as bacillus subtilis and other soil based organisms.
you dont "eat manure" you eat produce that has been fertilized by composted manure, a HUGE difference. the organisms that compost that manure are tuned by nature to eat rot and shit, thats not what humans need.
plants continue to emanate the same radiation signature they emitted while on the vine, it just gradually weakens as time goes by. i will try to find some research to back that up, dont have any at the moment.