In G35D Devkit, lane2 is selected (SW6 - Bit3 - ON) for USB0 and refclk2 (52MHz), which is sourced from the clock synthesizer OUT3.
Please make sure to properly configure the clock synthesizer, refclock & Input freq (Vivado) and the lane in dts & hardware. Configuring the clock synthesizer is done in FSBL (refer the FSBL patch) and for clock customization refer section Clock Synthesizer from the software user guide.
For further inquiries, please get in touch with mktg@iwave-global.com
Please find the detailed G35D product information in the below link,