These connections should be investigated--especially the single connector for the servo that operates the secondaries. That single connector (circled) would seem to be routed back to the black boxes you are examining. Also look for nicked, cut, smashed wires, and dirty connections in those areas.
Might be worth getting the TPS jumper from Kawasaki for reading the TPS voltages. By the way that butterfly shaft is operating erratically during initialization, there appears to be an intermittent connection somewhere. By measuring and reading the voltage at the secondary TPS, I'm suspecting it'll point to the wiring going back to the ECU. Could say even the ECU, but your vids show there is a connection problem.
Here is that jumper I use for my former Z1000. The part number for the harness you need is in the Kawasaki manual.