I have been watching the Initial D anime, but still haven't read the manga. How far does the anime cover, in respect to the manga? Are there any manga or anime exclusive content?
Altough the series stays pretty loyal to the story as told in the manga, there are a few exceptions. But these don't influence the story that much. One of the biggest factors affecting this is that a lot of the story in the manga got cut out.
We Initial D fans love those little details. It's a shame they had to cut out so much in order to fit one race in each episode. Watching Fifth Stage almost feels like watching an extended version of Battle Stage... And for that reason, it's strongly recommended to read the manga after watching the anime. That way, you don't miss all the details from the original storyline. - ID fan forum
As to where to how much it covers, Fifth Stage episode 4 ends at Chapter 499. (I stopped reading at chapter 501, so I ain't too sure how far the rest of this season covers.) I do know that the new season Initial D final stage will cover the left-over chapters, making this series fully covered by the anime.
With this said, there is a ton of manga-exclusive content: like I said, a lot has been cut-out in the anime. There is also some unique anime content (fillers) in the series. A few I remember would be Initial D Episode's 13, 22, and 23.
There might be some more but I couldn't find a source to confirm this.