Powering an USB to Serial from USB
That is not easy to do. You could try diodes and mosfets as switches, but one way or the other, there will probably some leakage current. The 6N137 requires power for the receiving signal.
Other common optocouplers might have leakage current in the nA range for the transistor output. That might be possible. Connect the GNDs. The RX and TX via optocouplers. DTR to RESET with 100nF as usual. Maybe you don't need extra inverters when the transistor outputs are used as emitter followers.

Could you make your project with the ATmega328P without the usb-to-serial module ? The Arduino Pro Mini does not have a usb-to-serial either.
Now that I mention the Arduino Pro Mini: Instead of making an Arduino compatible circuit with a ATmega328P, you could also buy a Arduino Pro Mini 8MHz, and remove the voltage regulator and the power led. Then you have the same thing.

That breadboard Arduino tutorial has +5V connected to AREF. Please don't do that. Keep AREF open, or connect a capacitor of 100nF to it to reduce some noise for analogRead.

In the deepest sleep mode, the ATmega328P can run more than a year on three AA batteries. The timer of the WatchDog can be used to wake up.
The voltage of the three AA batteries is directly connected to the VCC of the ATmega328P, without voltage regulator.

A very good tutorial about power saving is this: Nick Gammon about power saving