Yosemite and El Capitan USB crash kills keyboard and trackpad
The start up sequence is kind of hard to emulate other than actually power cycling the computer. 

I don't have a good answer since his failure is extremely low level, but here are the things I would do to troubleshoot and isolate things before considering a total reinstallation of the OS:


run sysdiagnose script each time a failure happens to capture the logs and also gain a sense of how often this happens. 
verify that plugging in the USB keyboard does not kick start the system properly for internal or external keyboard function
log out the user using kill -9 -1 or via remote screen sharing


My guess is the logs will show USB errors indicating a hardware fault, but that would need a look at your specific logs. It's not clear why you are manually loading the kext so perhaps I'm missing some information?