Very good question. I know the first two sound good. The second phrase gives more emphasis to the fact that the action is in the past (She isn't pissed off now), where as the first phrase doesn't really let us know if the girl is still pissed off now. The third isn't correct. You might need an ESOL teacher or an English professor to explain further.

It will be the first one that is correct. The second is not a tense at all. It's either "having been" (present perfect) or "had been" (past perfect) not both. The third is past perfect but is constructed incorrectly. To use it, you would have to include two things: a subordinate conjunction and the noun. It would have to read like this: "After she had been pissed off..." The sentence has two clauses. One is independent and forms a complete thought: She killed the mouse when it walked in. The second is called a dependent or subordinate clause that does not form a complete thought: "After she had been pissed off..." The word AFTER is what links the subordinate clause to the independent clause and is thus called the subordinate conjunction. The subordinate clause, in this case, is called an adverbial clause. An adverbial clause describes How, Why or When an action occurred. In this case, the adverbial clause describes when. So, what was the action?: "She killed the mouse." When did she kill it?: after she had been pissed off. (technically, you have 2 adverbial clauses [when he walked in] but we are going to ignore the second one for this explanation. So, our new sentence becomes: "After she had been pissed off, she killed the mouse when he walked in." But we can shorten the adverbial clause even more by using a past-participle clause. A past participle clause is formed with the verb have+ing and the past participle of the verb, in this case "having been". When using a past participle clause, you no longer have to include the subordinate conjunction (after) or the subject (she). So: "After she had been pissed off" becomes "Having been pissed off" "Having been pissed off, she killed the mouse when he walked in."