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QWhat do I do with the W2 or E or X or L or T wire?

AIn most cases these wires are not used and should be individually taped off. The W2 wire is for 2nd stage heating or heat pump auxiliary; E wire corresponds to the W2 wire for the GemTech thermostat; X wire sometimes corresponds to the C wire which is 24AC power; L wire is an indicator furnace monitor and a GemTech thermostat does not use it; T wire is an external thermistor and a GemTech thermostat does not use it, so it can be taped off.