...pretty sure you have broken the 2 "fundamental rules" of high speed PCB design:
1) keep track lengths SHORT SHORT SHORT!
2) keep tracks on the SAME layer along the path (vias cause large impedance variations in the transmission line - which cause EM to be radiated...)
Think you should consider a board re-layout with those in mind - place the USB device RIGHT NEXT TO the connector and put the tracks on the UPPER layer with a signal ground plane on the NEXT layer beneath.
While you are at it, DONT let the tracks cross over any ground plane boundaries - if you do, the return path for the signal has to run around the edges of the ground planes to "get home", which forms a great loop antenna \ signal radiator, emitting loads of EM interference...
Other tips - maximise clearance from other parts of the circuit - and if you are using ground plane on top of the PCB too, "stitch through" to inner ground layers regularly (every 3-5mm?) with small vias to keep the ground impedance low... its just like laying out for RF (VHF\UHF?) , so you may pick up some tips from websites dealing with this too...
If you are using TDR I guess you have already done the track calcs to ensure the correct track impedance for that type \ thickness \ dielectric of PCB material?
Non-obvious one - if any SMD components on the tracks have large pads, REMOVE the ground plane under these, as this also causes track impedance variation...
Also, try to use small SMD components to reduce pad impedance effects (0603, or 0402 if you \ your board assembler can stand it...)
Haven't done <much> USB layout myself, but have done quite a bit of high-speed digital video (270 - 1485Mb/s) so I think the same ideas apply.... I wish someone had told me all this 25 years ago, as it would have saved me a ton of hair-tearing and ditched PCB versions...!
Some \ all of the above may already be known to you - but it may help other readers...
Anyone else have some experience of high-speed layout like this? I would be grateful for any comments \ corrections on the above, as we could all benefit from this kind of info...?