There will be all sorts of problems with pops and thumps. Some of the switching signal will be coupled to the audio, and it may give rise to pops and clicks if you feed a low level signal from a guitar directly to the 4066.
It would be a good idea to amplify the signal to a volt or so first. Secondly it would be a good idea to arrange that the switch always operates as the audio crosses zero going positive, to avoid clicks from sharp edges and thumps from dc level shifts. I,ve got someone worrying me for one of these, so I,ll be developing the circuit shortly, and I'll be able to send you the circuit privately in a couple of weeks. I think it might use a couple of 7555's , a tl082 and a 4013.