I took a break from trying to troubleshoot the ESP8266 and started planning out my circuit board. I started having more troubles with the 16 channel analog Mux. I realized that if I used the same 8 channel mux as TRAVIS II, that I'm much more familiar with, and read the remaining analog pins on the arduino, then I still have the same number of analog sensors that I initially wanted. So I altered the arduino code for that. Maybe I'll look at the 16 channel Mux again in the future.
I tested the IR with my quad level shifter. It's supposed to be able to shift the voltage both ways, 5V to 3.3V and 3.3V to 5V. But I couldn't figure out how to shift it up to 5 for the IR sensor. Then I realized that if I got a 5V arduino pro mini, the only issue would be the LIS3DH and the ESP8266 which are only 3.3V. I decided to try the LIS3DH with my Arduino Uno, hooked up to the 5V and the level shifter. That was a mistake. I didn't hook it up right either and completely fried my accelerometer. Now I have to wait for a new one in the mail.....
I also ordered a different level shifter that Sparkfun specifically has a tutorial on how to connect the LIS3DH to it. That way if I do switch over to the 5V Arduino, then I'm less likely to mess up. For now I'll get by with 3V only and the IR sensor will just not work ass well as it could.
If you are looking for a summary for my Masters thesis, it is here.