Thanks for the stack trace. I took a quick look at the code from the trace and, unfortunately, found a bug: the call that is causing the NPE is trying to use a DiskInitFile that has not been created yet; in fact it is in the process of being created lower in the call stack (DiskInitFile.<init>).
I wonder if there is a workaround. Would you describe how you're doing the upgrade, or, if you've done that in the support ticket already, reference the support ticket number?