@dontteleport as your post is very long, with no summary provided, I've not had time to read it.
However providing the minimum connection time was met (which it sounds like it was) then EMR see contractually obliged to honour the ticket; furthermore if you are delayed by 15 minutes or more, you are entitled to delay compensation.
In future, if possible I recommend booking any such journey as a through journey, through an accredited site, such as ourselves, which would provide you with evidence of a contract covering the entire itinerary.
Also if you end up in a dispute in future, it is very helpful to keep the post concise, and include the itinerary of your intended journey in a list/tabular format. If it's a long post, I suggest including a brief summary.