OK, so the Page Pack does have a value for skuid__MasterPage__r.skuid__UniqueId__c, which is good, because that’s the only reliable way to identify the same Page in two orgs. Looking at your Post Install script though, I see the issue: the tutorial is out of date as of Banzai. The gist of it is that version of the script doesn’t account for the Master/Child page functionality because it was written before they existed. After doing the initial upsert of all the Pages in the Page Pack, you have to go through all the Child Pages and associate them with the correct Master Page (which may not even be in the Page Pack). We’ll get the tutorial updated, but that’s the overall strategy.
