What does 翻了个儿 mean?
可毒瘾一发作，他就不停地流眼泪，流口水，哈欠连天就，接着便浑身冒冷汗，颤抖，肌肉疼，骨头疼，{心呀、肝呀、肺呀什么的，全都翻了个儿}，真是求生不得，求死无门。


全都 refers to 心呀、肝呀、肺呀什么的, not all the symptoms.

翻个, turn over, defined in baidu baike:



翻个
fān gè
翻过来；颠倒过来：场上晒的麦子该～了。


了, in 翻了个儿, denotes a completion, as you know. 儿 is erhua.