In usb section the recommended USB EMI common mode coke is ACM2012D-900-2P.The cutoff frequency for this feed through is mentioned as 3.5GHZ from the datasheet but the third harmonic frequency of the USB 3.0 Signalling will be arround 7.5 GHZ will this part be ok or we need to go a head with parts having similar spec with higher cut off band

The key character of USB3.0 common mode choke is the Max Scc21 @ 2.5GHz and Min Sdd21 @ 2.5GHz as you can see in page 23 of OEM DG. As the energy stored in harmonic frequency is much low, no need to care much on it. Just follow the Common-mode Choke table in page 23.