Electronic – Logic gates not working as expected

EDIT - because of my misinterpretation of the circuit I'm editing the answer to focus on the output of the sensor - are you using the analogue output to feed into the inverter - if you are maybe you should try a Schmitt trigger like a 74HC14

For your first problem, whether or not your ATMega328p is attached to the USB to TTL serial converter is irrelevant; if it is showing up in Device Manager, then the computer-to-converter connection is functioning properly. Every serial device should also show up in the Arduino IDE. Since it is not showing up in the Arduino IDE, I'd check Device Manager first; if it's not there, then you most likely have a faulty USB-to-TTL-Serial converter. Those CH340G board are really cheap and -- well, let's just say, you get what you pay for.

Note: I've seen at least one version of the board that has a jumper on it that lets you drive the I/O voltage with either 5V or 3.3V, which is super handy. If you forget the jumper, it ends up not powering the CH340G at all, which would cause Windows/Arduino to not detect it. Here's a picture of the CH340G board I've seen the jumper on before:

Now, once you get the device detected in Device Manager, it should be detected in Arduino's IDE as well; if not, restart the Arduino IDE. Once it's detected, you should be able to program your ATMega328p with the USB-serial board with one very important caveat: you must pull the reset line low right when you program the chip to manually reset into the bootloader. This is because your board does not have the DTR/RTS signals which Arduino Uno uses to pull the reset line low.

If that doesn't work, check to make sure you actually know what you're doing, with respect to breadboard connections. The ATMega328 is a pretty crappy MCU; you need an external crystal, decoupling capacitors, and a pull-up on the reset pin just to get it doing stuff (though it does have a slower, inaccurate 8 MHz oscillator, but without modifying the bootloader, you won't be able to use it).

Second problem: I assume your USB-to-serial converter is operating at 5V I/O levels; when you drive a 5V signal into a 3.3V MCU like the ESP8266, the protection diodes kick in, and limit the signal to about 3.6V or so (depending on the forward voltage of the protection diodes). You should never directly-drive 5V signals into a 3.3V part (even if it says it is 5V tolerant). I would run the TX signal through a 1k resistor into the ESP8266's RX pin. This will make it "easier" for the protection diode to clip the signal. Or, you know, you could just get a 3.3V USB-to-serial converter. I keep a stack of both laying around.