On the Orchel Trading Route quest, I accidentally built the storage first and now Darude is in the storage and some merchant is in front of the castle but I didn't talk to Darude yet so now I can't progress on the quest.

Building the storage and the upgrade for the quest in Orchel are two different things. That the guy in front of the castle changed normally means that you made the upgrade already, so maybe it's just not marked green in your quest log but you can advance your quest?