Hmm, could be VoodooInput.kext that's making the difference because I switch it to the latest VoodooPS2's Input.kext in the Config file instead of what you had before which was Input.kext from VoodooI2C (older version).
You could try putting back the latest VoodooPS2 but switch to VoodooI2C's Input.kext to confirm.
The ethernet on the dock, do you know what model or brand is it? Maybe need to add a kext if existed?
For thunderbolt, give this SSDT a try, just add it to the Config file. As you know, it'll only work on boot if it works at all, but not hot-plugging.
Post a new IOReg file after adding this SSDT file
SSDT-TYPEC.aml.zip