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"?
Can 'desculpando' also be used as an adjective? i.e. a person who is forgiving?