I wish to revitalize this topic. I am having the same issue, but I consider scrapping my character for someone else's to not be a solution. I have tried all of the "console" advice I could find. It just seemed to break my MQ progression. Meaning I received no quest updates using completequest mq07, and it wouldn't do the set stage commands either. This topic is 6 years old, and I'm hoping that by now someone has a real solution to this glitch.
Edit: Ok, so I figured this out. It's mods that cause this problem. Some mods have info related to oblivion and this messes with Nehrims' scripts, I believe. For me, I thought it was my fault by converting tes4 mods to Nehrim. For one of them this was the case, so I used tes4edit to remove the remaining Oblivion related info. For the record, 'Jasons pirate ship' unfortunately has some problems with MQ07 that I couldn't fix, but I theorize that it could be installed after MQ07 is completed. Too bad, it's a great sailing mod... So really, if you have the same problem with this quest, this is probably why.