I think that for a counterfactual conditional like this, you need to relate it back to the actual situation, as follows:
"If I were you I would have done that -- but I am not you, so I did not do that (since I am not you, I could not do that)."
As you can see:
"I am not you" refers to a general truth, a situation that holds over a long period of time, past, present, and presumably future.
"I did not do that" refers to a situation at a particular time in the past.
"If I had been you I would have done that -- but I was not you so I did not do that (not being you at the time, it was impossible for me to do that)"
As you can see:
"I was not you" refers to the situation at a particular time in the past -- the specific time that is under discussion. The meaning is "I was not in your shoes at that time".
"I did not do that" also refers to the situation at that particular time.
The difference is fairly clear.
"If I were you" refers to a general hypothetical situation, that of me being in your position.
"If I had been you" refers only to a hypothetical situation at a particular time in the past. The meaning is, "If I had been in your shoes at that time".
This might seem like nitpicking, but a clearer distinction can be drawn with other examples.
"If I were a vampire, I would have sucked his blood."
This refers to a general situation of me being a vampire. Since I am not, in fact, a vampire, I did not suck his blood.
"If I had been a vampire, I would have sucked his blood."
This refers to a situation of being a vampire at that particular time. Since I was not a vampire at that point in time, I did not suck his blood.
This could conceivably be said if the speaker regularly switched from being a werewolf one month to being a vampire the next. In other words, it might simply have been bad timing in his cycle that he was unable to suck the victim's blood that particular month.
"If I had a gun I would have shot the intruder."
Straightforward -- if I were the possessor of a gun I would have shot the intruder.
"If I'd had a gun I would have shot the intruder."
Regrettably, although I own a gun I did not have it with me at the time, so I was unable to shoot the intruder.
"If I weren't married, I would have seduced her on the spot."
But I'm a married man, so I didn't seduce her.
"If I hadn't been married, I would have seduced her on the spot."
The speaker could be divorced now, but at the time he was still married so he didn't seduce her on the spot.
This distinction could be applied to all kinds of situations.