The gear in your video is the starter clutch; the large metal piece is the flywheel and alternator rotor.
The best tip for removing those stubborn JIS fasteners is using an impact driver (the whack-it-with-a-hammer type). You should be able to get them out even using a Philips bit. I have 10mm hex-head screws in my bike for the starter; if you're not super worried about originality, that's a good plan.
KZ440s didn't come with kickstarters at all (despite what the casting on the clutch cover says), so at least you know the previous owner didn't remove it. Would've been nice of Kawi to leave it IMO, but I can understand the thought. 12V bike electrical systems were getting really common and reliable, so they didn't need to have the backup in case of failure. They just didn't necessarily bank on these bikes lasting 40 years, lol.
Good luck with your build!