I am using Arduino UNO Rev 3.0 for one of my project and proved POC. After that i redesigned the arduino onto the PCB, but when I connect USB the port in the IDE is grayed out.
Checked for the shorts
Checked for the USB voltage ( USB - 5V, D+ - 3.1V)
Here in my PCB I used ATmega16U2-AU for USB-to serail converter and ATmega168PA-AUR.
Sounds like maybe you need to install the firmware on the ATmega16u2. If the firmware currently loaded includes DFU (Direct Firmware Update) mode you should be able to use the Atmel FLIP program to upload new firmware. Here are instructions:
If the DFU firmware has been overwritten you will need to use an In-System Programmer (ISP) like the USBasp or USBtinyISP to burn fresh firmware. On my Mac the firmware you want appears to be this file: /Applications/Arduino.app/Contents/Java/hardware/arduino/avr/firmwares/atmegaxxu2/Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex