MSD pickup wires

Jim Ward said
timing seems to be jumping at idle.

Are you using a dial-back timing light? Dial-backs read erratically/inaccurately on MSD ignitions.

Jim Ward said
If they are backwards and the polarity is reversed will I need to change the plug wire orientation if I flip flop the wires?

No! Assuming you have the firing order correctly set up and there are no phasing issues on your distributor, the pickup polarity has nothing to do with firing order.