@archw XenClean is not needed when upgrading; it's only needed when switching tools vendor, or when switching from the old XCP-ng 8.2 tools.
The XCP-ng 9.1 tools installer will block installation and indicate an error whenever XenClean is needed.
@kruess I can see numerous instances of VM_HOST_INCOMPATIBLE_VERSION in your xensource log. It is difficult to know the exact cause ithout more details.
Was the pool master restarted after the patches were applied?
Are you trying to start the VM on the master?
Are you upgrading directly from XS 7.1.2 to XCP 8.3?