ESP12F (esp8266) every program is running okay but it's warm/hot
It's absolutely normal for an ESP to become warm a little bit, especially if wifi is active. If the metal shielding gets up to 30 or maybe 40 degC I wouldn't worry too much. I suggest you measure the current/power consumption. From my experience, an ESP in a typical application (wifi enabled, some peripherals like LEDs or transistors attached) draws around half a watt. When I power my ESP-based boards for the first time, that's what I measure to have an idea if there's something wrong.
And no, the IOs are not 5V tolerant.