The green LED issue must have happened when you pulled or replaced the LEDs. Do diode tests on all the pins of the RGB LED (the square pad is ground). The green pin is the one connected to R19 (the pin between the square pad and the pin closest to the ISP header). Use your continuity tester to check for shorts around the LED. You can also make sure the other side of R19 is going high when the green LED should be on.
Good luck.
-Brach