I tried this minimum configuration and it works fine. I am using TWR-K65F180M so Oscillator is used but theorically it must be the same configuration for you.
It is important to connect VBUS (from USB connector) to VREG1_IN (so, i noticed that you already did it.) Please, try this simple code and let me know if PLL is still not locking.
MCG_C1 |= MCG_C1_IRCLKEN_MASK;
OSC_CR |= OSC_CR_ERCLKEN_MASK;
SIM_SOPT2 |= SIM_SOPT2_USBREGEN_MASK;
SIM_SCGC3 |= SIM_SCGC3_USBHSPHY_MASK;
SIM_USBPHYCTL = SIM_USBPHYCTL_USB3VOUTTRG(6);
SIM_USBPHYCTL |= SIM_USBPHYCTL_USBVREGSEL_MASK;
USBPHY_CTRL &= ~USBPHY_CTRL_SFTRST_MASK;
USBPHY_CTRL &= ~USBPHY_CTRL_CLKGATE_MASK;
USBPHY_TRIM_OVERRIDE_EN |= USBPHY_TRIM_OVERRIDE_EN_CLR_TRIM_DIV_SEL_OVERRIDE_MASK;
USBPHY_PLL_SIC |= USBPHY_PLL_SIC_CLR_PLL_POWER_MASK;
int crystal_val = 16000000;
if(crystal_val == 24000000)
USBPHY_PLL_SIC &= ~USBPHY_PLL_SIC_PLL_DIV_SEL_MASK;
else if(crystal_val == 16000000)
USBPHY_PLL_SIC |= USBPHY_PLL_SIC_PLL_DIV_SEL(1);
else if(crystal_val == 12000000)
USBPHY_PLL_SIC |= USBPHY_PLL_SIC_PLL_DIV_SEL(2);
while (!(USBPHY_PLL_SIC & USBPHY_PLL_SIC_PLL_LOCK_MASK));
i++;