Hello Anon,
1. If you had woken me up, I wouldn't be late for my appointment. (I can't say "If you woke me up, I wouldn't be late", can I?)
— You're right: "if X had happened then, Y wouldn't be the case now."
2) If she was qualified, She would've got the job.
— The if-clause here relates to the true past: we don't know if she got the job, or if she is now qualified.
Cf.
2a. "If she was dead on arrival, she would have been put straight in the morgue. So let's go and look for her there."
But "she was" in the sentence may also stand in place of a subjunctive, e.g.
2b. If she was were qualified, she would've got the job.
— i.e. if she were qualified now, she would have been qualified yesterday, and would have got the job. (But since she isn't qualified, she didn't get the job.)
3. If I knew them really well, I would have gone to the party. (So I still don't know them well?)
— You're right. Cf.
3a. If I had known them then as well as I know them now, I would have gone to the party.
Let me know if you need any more help!
MrP