Just an FYI,
The USB bus can be sent to the mPCIE header via a GPIO on the RouterBOARD 912. This way you can toggle between true PCI and USB ( LTE modems and such ) via the mPCIE header.
Looking at the older RB91X definitions:
#define RB91X_SSR_BIT_LED1 0
#define RB91X_SSR_BIT_LED2 1
#define RB91X_SSR_BIT_LED3 2
#define RB91X_SSR_BIT_LED4 3
#define RB91X_SSR_BIT_LED5 4
#define RB91X_SSR_BIT_5 5
#define RB91X_SSR_BIT_USB_POWER 6
#define RB91X_SSR_BIT_PCIE_POWER 7
#define RB91X_SSR_BIT_PINHOLE 14
#define RB91X_GPIO_SSR_STROBE RB91X_LATCH_GPIO(0)
#define RB91X_GPIO_LED_POWER RB91X_LATCH_GPIO(1)
#define RB91X_GPIO_LED_USER RB91X_LATCH_GPIO(2)
#define RB91X_GPIO_NAND_READ RB91X_LATCH_GPIO(3)
#define RB91X_GPIO_NAND_RDY RB91X_LATCH_GPIO(4)
#define RB91X_GPIO_NLE RB91X_LATCH_GPIO(11)
#define RB91X_GPIO_NAND_NRW RB91X_LATCH_GPIO(12)
#define RB91X_GPIO_NAND_NCE RB91X_LATCH_GPIO(13)
#define RB91X_GPIO_NAND_CLE RB91X_LATCH_GPIO(14)
#define RB91X_GPIO_NAND_ALE RB91X_LATCH_GPIO(15)
#define RB91X_GPIO_LED_1 RB91X_SSR_GPIO(RB91X_SSR_BIT_LED1)
#define RB91X_GPIO_LED_2 RB91X_SSR_GPIO(RB91X_SSR_BIT_LED2)
#define RB91X_GPIO_LED_3 RB91X_SSR_GPIO(RB91X_SSR_BIT_LED3)
#define RB91X_GPIO_LED_4 RB91X_SSR_GPIO(RB91X_SSR_BIT_LED4)
#define RB91X_GPIO_LED_5 RB91X_SSR_GPIO(RB91X_SSR_BIT_LED5)
#define RB91X_GPIO_USB_POWER RB91X_SSR_GPIO(RB91X_SSR_BIT_USB_POWER)
#define RB91X_GPIO_PCIE_POWER RB91X_SSR_GPIO(RB91X_SSR_BIT_PCIE_POWER)
#define RB91X_GPIO_PINHOLE RB91X_SSR_GPIO(RB91X_SSR_BIT_PINHOLE)
The PCIE GPIO was +1 from the USB ( so probably pin 62 ). I remember if you brought the USB header GPIO high, then the MPCIE Power GPIO needed to be low. If you wanted to bring USB to the mPCIE header, you would set the USB GPIO low and MPCIE GPIO high.
Since your USB GPIO looks to already be high, check the MPCIE GPIO and verify it's low. You may need to add a "gpioswitch" definition and label it mpcie_power_switch and set it to pin 62 and default 0.