1) If you’re already strong in the hills, I wouldn’t focus on training MORE on the hills
the recommendation I’ve seen is to do intervals/efforts uphill. Is this still where I should be focusing?
2) If the flats are where you can improve the most, then that’s where I’d focus.
I do struggle getting my legs turning over on the flat after a climb (feels like a triathlon transition) – is this an ME issue?
As you’ve identified, it sounds like ADS to me. You’ve got a strong and efficient system for short powerful sections of a run but the long and low intensity is where you’re coming up short.