I re-ran the dnf distro-sync command from qubes-dist-upgrade-r4.3.sh to remove the old kernel-qubes-vm version. I then manually ran more commands from Stage 3, basically what was described in Qubes-dist-upgrade stage 3 grub2-efi install failed - #4 by vwrto and Qubes-dist-upgrade stage 3 grub2-efi install failed - #5 by vwrto.
I ran these commands and saved the screensaver package swap for later.
After this, I was able to reboot into Qubes 4.3 but I encountered a new issue: 4.3 upgrade Error: Check of pool qubes_dom0/vm-pool failed. I don’t believe the new issue is related to this Stage 3 failure, so I created a separate thread.