I have two 120v duplex receptacles on my GEN4065 4000watt portable generator and I have ourchased a Emergen 6-5100A 5000 watt manual transfer switch which has a 4 prong twist lock plug. How can I wire the generator to the transfer switch to the generator?

The generator that you have is not designed for connection to a transfer switch. I went through the manual and saw the two 20 Amp 120 Volt receptacles as well as the DC receptacle.

This is a small portable generator that is used for a camp site or tailgating.

The only available lines you could use in a residence are from the two 20 amp circuits. And you would need the correct type cord (one is provided in the packing) to connect these receptacles and then feed the two possible circuits in the home.

You cannot use this unit to operate off a transfer switch to a panelboard.