I know Sorcery from goanimate. He is a youngling and not had chance to watch every series 12 times over. I think for what he has learned of Trek so far the premise is actually rather good.
It does need a lot of tweaking, but I believe the journey to find the borg's origin fascinating. I think there has to be a driving reason why they would do this. Watch Times arrow. The TNG crew find a 500 yr old head belonging to Data. They embark on a mission to find out where it came from. They end up travelling in the past. Without the head they wouldn't have gone on the mission. The head was very important- because it belonged to the crew and they were emotionally invested in data's well being as much as trying to unravel the mystery of the 500 yr old head.
You have to come up with a plausible reason that would drive the Commodore and the crew to pursue this investigation.
I also think you have been influenced a lot from reading the script of my series I am currently working on. I think you should forget the things I have done and make yours stand alone. Having the mission a cover up for the real mission doesn't serve this story. Whereas in mine it serves as a way to propel the story into a different direction plus it involved section31 hence a cover up.
You don't need to do that. Your mission is clear and clever enough to not need to add things that will detract from it. Focus on why the crew want to learn of the Borgs origins. As a series it could have many stand alone episodes whilst they investigate.