Can you explain why this takes so long? I accepted the position with DoS in August, submitted that huge background check document shortly after, sent in the fingerprints and whatnot and have only been contacted twice for further information and that was like 2 months ago that I last heard anything. Is it normal to wait 5+ months?
It's normal to wait upwards of a year.
The problem is that there's, frankly, too many people with security clearances that don't need them. Originally, OPM worked investigations - but then they spun off an agency a few years ago (NBIB) and now they're getting ready to spin it off to DoD. The problem is that there just isn't enough investigators. The government relies HEAVILY on contractors (about 90% of all investigations are done by contractors). Things got worse in 2014 when they abruptly canceled the contract of USIS (my old company), which had about 4,000 investigators nationwide. Yeah, they laid off around 4,000 people - and it didn't even make a blip in the national news. The other contractors have never been able to pick up the slack.
Investigations take time - they have to interview people you list, and find people you didn't. They go to where you lived, they go to old jobs, they do law checks in ever city/state you've lived/worked. Then when the reports from all over the country are finalized, they're internally reviewed by contractors at two different levels, then the government reviews it, then the specific agency you work for reviews it. If, at any point in the process, any reviewer has a question... they kick it all the way back down to the investigator and the whole thing starts all over again.
Depending on your agency, you're likely to be granted an interim clearance that'll let you get started. Because the wait is so long. And to make matters worse, if you hold an active clearance - you have to go through the whole process every 6 years (it used to be 5 years, but they changed it to 6 because the backlog was so insane).
Basically, the entire security clearance industry is a goddamn joke and the public largely has no idea. It's insane. You'll be fine, though. Everyone goes through it. It's a long wait, it's a huge pain in the ass, but everyone can commiserate because everyone goes through it.