The not knowing will keep me up at night...

It depends on where you are, or where your audience is. In US usage, small punctuation marks (commas and periods), must go inside of the quotes, no matter what the sense of the sentence. That would be your second version above.

To my understanding, UK usage (I'm not sure whether Australia does the same) is that the location of the punctuation depends on whether you are actually quoting the punctuation or whether it applies to the sentence as a whole. In this particular case, it would go after the closing quote. However, either way, I think it needs to go inside of the parentheses, so you need a third version:

In Irish/UK usage, the full stop goes OUTSIDE the close brackets normally.

However, if the whole sentence is in the brackets, then the full stop goes inside it too.

So:

I always loved eating onions (even though they repeat on me dreadfully).

vs

I always loved eating onions. (Mind you, they repeat on me dreadfully.)

The full stop goes outside the inverted commas.

Tracy is correct. This is true in US writing as well.