Data will be sent to a Raspi to be logged. This will also re-transmit the data to another arduino similar to the one above.
Is it safe to assume that MCU has built in charging when supplied from a USB?
Can you see anything I might have missed or could be changed?
That module includes a charger for the battery and automatically switches to charge mode when USB is connected.
Without knowing what you are trying to do with this setup, and what other bits you already have, it is difficult to know what might be missing. If this is the thermocouple you are referring to
then you have listed enough bits for a remote temperature monitoring station, assuming you already have a thermocouple and you will print your own case. What are you planing to use the DAC for?
It does have a charge IC but there is also nothing limiting the discharge of the battery. There are lots of methods used, the most common being placing the 8266 into deep sleep to try and prevent over discharging the battery.