Can I translate it to "Why are you excusing yourself?" or would that only be viable if I replace the "se" with...what was it? "si mesmo"?
yes, that's another suitable transation.. "por que você está desculpando a si mesmo" would not sound good.
Would "for what are you apologizing?" be correct as well?
Not sure, but perhaps "pelo que você está se desculpando?"?
"what are you apologising for"?