if low latency is your concern, the out/in routing with a physical cable is not a good option because this adds the output buffer latency and the input buffer latency together.
if you are using ASIO then have a look at Jack Audio, this allows to make audio connections between audio software. its not easy to setup, but with some minutes of doc reading it works pretty well.
what is your goal in the end? will the music be played from the same computer or will it be an external audio source?
the noise on the audio input is pretty normal for mic inputs and cheap cards. if you use a line level input it should be much better.
the vvvv FFT is a bit different to the standard FFT, this is also normal. it has a different frequency scaling. i haven’t compared the two algorithms step by step yet.
in the end latency comes down to buffer sizes… so check these first on every option you are trying. have a look at the old FFT4Channels node, it has a FFT and AudioIn inside which are configured to have lowest possible latency.