Recording signal from arduino as an audio file

My issue is, I don't have or know how to generate the .wav files.

Well read the link on the wav file format. Basically you just need to add a header to your data.

However your problems do not end there. Encoding data onto an audio sub carrier is not done the way you are going about it. Amplitude modulation is very error prone, you are better off with phase modulation. Look up how old school slow modems modulated data.