This one ran for more than 36 hours on my laptop with ghidriff's SimpleDiff (mostly single threaded so I don't think a bigger machine would've made much difference). I just filed a PR for an optimization that seems to make one phase run in seconds instead of hours, that sounds a bit too good to be true, so reviews are welcome:
https://github.com/clearbluejar/ghidriff/pull/107/cc
@clearbluejar