Congrats on keeping at it and getting the initialization to work at least, these things can be frustrating
Just to verify that in the quickshifter settings, both the up and down are enabled and then initialized?
After you select "EQUIPMENT" then "QUICKSHIFTER" ON, you have to return to "SETTINGS" then select "FUNCTION" then select "QUICKSHIFTER" in that menu and enable "UP" and "DOWN" to turn on quickshifter functions and set levels for both and then return to "SETTINGS" and "INITIALIZE QUICKSHIFTER" to start that process again.
This is sort of opposite of how the CRF1000 does it with eanbling and adjusting up / down in settings after initializing.
Not sure what you have instruction wise so attached the QS installs for CRF1000, CRF1100 and the CRF1000 Accessory Guide for details on how the QS settings are done on the 1000.
Is your SCS jumper secure and not intermittent when starting the bike and such?