[Help needed] Thunderbold firmware disasembly for debuging

Hi everyone! After some Intel Thunderbolt docs were released on the web, I have decided to modify some thunderbolt firmware to make a ATTO Thunderlink to work not only at x4 mode, but also with 2 x2, or 4 x1 mode with custom PCIe PCB with Clock Generators, by switching Lane Width mode with CS signal switching to be able to select SPI firmware. Anyway yet have no luck, and I think that there are some additional code exist in uCode (Patches) of port firmware.

SO THE REQUEST IS: How is the best way to disassemble the TBT firmware? And disassemble properly!?

I have tried with Hopper Disassembly and Binary Ninja, IDA FREE not support X86 instructions.

Tried with Hopper v4, v5 and Pseudocode is very different:

Thanks!

uCodes and Firmwares attached

Firmwares.zip (4.5 KB)
uCodes.zip (3.2 KB)