Is it permissible/optimal to short the left (tip) and right (ring) contacts of the Maestro's LINE IN jack to the output of a SignalLink USB or should I just pick left or right. Of course, the sleeve is connected to ground and I know not to short the sleeve to either tip or ring.
First, do not short the tip and ring. The LineIn input is a pseudo balanced input. Shorting tip to ring is shorting LineIn+ to LineIn- If you only need to use two wires, use tip (+) and ring (-) and leave the ground disconnected. If you have 3-wires, then it is tip (+), ring (-) and ground (cable shield) and do not connect anything together. The input is converted to unbalanced at the codec input.
Second, why are you using a SignalLink instead of DAX (unless you are operating remote)?
DAX performs a bit perfect transfer of audio data between the radio and the digital mode application, whereas a SingnalLink (or any other sound card) must do an analog to digital back to analog conversion which degrades the signal quality.
Also, the ADC/DAC in the SignalLink is not as high a quality as what is in the FLEX-6000, so in addition to signal degradation due to an unnecessary analog to digital back to analog conversion, the ADC/DAC is also degrading your signal to noise characteristics.
And the analog cabling between the radio/Maestro and the SignalLink increases the chances of getting RFI into the connected device whereas DAX uses no physical cables.
Unless you are connecting something like a Pactor modem (hardware) to the radio that requires using the analog audio inputs and outputs, no one operates digital mode applications using the FLEX-6000 using analog inputs unless you are trying to operate remote using the Maestro, which if that is the case, I can understand why you are doing it this way