Ok,
So after step 7 using USB2, it detects correct FX3 FW, bad FPGA GW, FX3 programming to Flash doesn’t give any errors but then it fails to boot from Flash.
The one more thing that you could try is programming FPGA GW first (maybe bad GW is preventing FX3 from booting somehow).
To do that after step 7:
a) In programming window select ‘Altera FPGA’ and ‘Bitstream to flash’ and click ‘Program’.
use GW from: https://github.com/myriadrf/LimeSDR-USB_GW/blob/master/output_files/LimeSDR-USB_lms7_trx_HW_1.4.rbf
b) After this the device will probably get reset so you will have to program FX3 to RAM again to check FW and GW version in device info.
c) If GW versions is no longer 0’s, try programming FX3 to flash again.
If all this fails, then I don’t have any more ideas.
Also, that issue with USB3 is strange, maybe there is something wrong with your board or power power delivery to board when using USB3 port.