ClickOnceToSquirrelMigrator
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Update.exe not found?
The squirrel app has included both Update.exe and Squirrel.exe, the ClickOnce app has both as well. But the are in the same directory as the app, it appears that it is looking for them in the parent directory which doesn't exist (from what i can tell in clickonce).

I've got the same error. This problem is caused by the UpdateManager, not the ClickonceToSquirrelMigrator. The issue I found is that if you don't provide application name for the UpdateManager (in the clickonce app) it tries to derive the name from the current application while assuming that it is a squirrel application (which it is not). So it looks for update.exe in the parent directory which does not exist.
A fix to this is to provide an application name, this way the update manager does not try generate it. Also it was helpful for me to specify the root directory. Otherwise when the squirrel app was installed it was installed within the clickonce path...which is probably a bad idea.