So we've gone from every 12 seconds to once a minute. I assume you are printing the ALIVE right after the Serial.begin().
The API docs recommend explicitly disconnecting from the peripherals like Wi-Fi before calling esp_deep_sleep(), so I would suggest you do that too, even though it is probably unrelated.
Maybe comment out all the Wi-Fi stuff and add some more serial debug. Then just test the reliability of the wakeup by itself. If ok, gradually re-add the Wi-Fi and test.