#1 is fine. That's the mixed type conditional: if this thing had happened (in the past), then (some present conditional or perfect conditional).
#2 is wrong because in standard English you never say "You was". If you change it to "If you were eating well...) it would be fine, because then it would be a present unreal conditional, of Type 2, using were because of the subjunctive mood. If you were eating well (right now), then you wouldn't be scrawny.
#3 is also fine! It's actually just Type 2 again: simple past + present conditional or present continuous conditional. The Type 2 can be used to talk about the present or future. Yes, it looks weird to use the simple past with a statement about the present or future, but in this context ate doesn't really refer to the past the way that had been eating does; it's the way we use the "simple past" to refer to a general hypothetical condition: If you ate well (in general, without any time reference), you wouldn't be scrawny.