Meaga works via USB but not by Vin or Barrel Jack -- > ??

The arduino was shorted unknowingly - 5v out with GND and the ardunio got hot and started smoking slightly. The arduino still works fine with the USB but not by Vin or the barrell jack (9v)
any suggestions what could be wrong??

I was thinking the voltage regulator however when its connected via Vin or jack the power on led comes on dimly and flickers thats all while on usb it works normally.

Thank you in advance - appreciate the support.

Sounds like 5V regulator or the reverse polarity protection diode is shot.
Both are replaceble with careful soldering.

Is there any way to check them before attempting to replace it?

It's gotta be the regulator (but that doesn't rule out the diode or other parts also being trashed), becuase Vin pin bypasses the diode, but you say it still doesn't work.