1. Anything >24 hrs is a stopover. Sometimes pure domestic US fares state >4hrs but that's specific to the US domestic market.
2. Originating is the trip origin ie first departure city.
3. Yes.
4. Correct; if it's ticketed it's either good or not but in that case it's not your problem.
5. Rarely but it's the carrier's responsibility (best examples are error fares).
Your itinerary likely used married logic which means I class was only available all the way through the journey while adding the legs separately one was likely unavailable and either broke the trip (fared separately for the legs) or simply priced in R/D/C/J.