Wow, more than I ever expected! I thought your USB-TTL chip would be dead, so bypass that and power it directly. Then maybe you could rescue the ESP8266 chip.
Your D5 pin is dead, very dead. If that's all, you're really lucky. I'd say disable it (on the physical level: cut off the pin from the PCB so you can't accidentally connect something to it and fry the rest), and just use the other pins.