This may seem like a stupid question, and probably is. Please bear with me. I have 1/4in. tip/sleeve connector jacks and 2-wire shielded audio cable, from which I intend to make an instrument audio cable.
The question: what do I do with the shield?
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Generally speaking a shield should not carry signal. It should be grounded at one end, usually the source but in this case probably at the input. That would mean connecting the hot signal line to the tip and the return signal line plus the shield to the 1/4" sleeve, assuming that the sleeve is at ground on the input, and leaving the shield unconnected at the source.
This is not ideal but without a way to separate chassis and signal grounds -- having only two conductors -- it's probably the best you can do.