I guess we have old quest and ley lines - all 5 added into those percentages.
Only quests that should advance us towards part 3 are:
"The Battle for the Sun's Reach Armory - Rewards 9 gold 10 silver, +250 Reputation *
Distraction at the Dead Scar - Rewards 9 gold 10 silver, +150 Reputation *"
Yes, these 2 and nothing more.