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Adj regulator has error in layout - SOT223 pins 1 & 3 are swapped.
D0 of 5V regulator module is to close to mounting hole. Rotate 45Deg, or convert to SMT diod and rotate 90Deg
Cutouts for enclosure are to close. Re-measure enclosure and adjust cutouts.
Board could be bigger in all directions by .10"
footprint for DS3231S is not SOIC16
HCNR200 A and D have an open between shunt resistor and input
For thermistor input switch to 10K in series with Therm and 10K parallel with therm to ground.
For analog input need input voltage divider to MCP6004 to reduce max input voltage to 2.5V