So why are you here alone and crying? If it’s not too much to ask.
I think you usually use if it’s not too much to ask when asking for a favor, but I could be wrong.
This is not correct, better would be:
So why are you here alone and crying, if you don't mind me asking?
You'd say "if it's not too much to ask" when you're asking them to do something. Here, you aren't asking them to do something, you're asking them how they feel.
You can compare it with this:
Can you help me open this jar of pickles, if it's not too much to ask?
By the way, "If it's not too much to ask" cannot be its own sentence.
You could move it before the comma, too, like the following which are identical to the previous examples:
If you don't mind me asking, why are you here alone and crying?
If it's not too much to ask, can you help me open this jar of pickles?