I also swapped from a Core V1 to the NR200, welcome to the club!
As for the HDDs, you can fit one of them on the PSU bracket if you don't want it to be on the side bracket. I had one that I use for backup mounted there, it's not connected because I couldn't bear the noise (and, actually, as it's only for backups it's better if it doesn't stay connected) but I'll manually plug it from time to time just to do a backup. I can easily recover it from the top, plug it to the cables at the front and then put it back in its place thanks to the tooless fixing mechanism:
https://i.imgur.com/hZz2zNO.jpg
Have you actually tested CPU temps with the Noctuas vs stock fans? I think I saw a review where they tried this and the stock fans were the best one for this cooler, and it looks like you could fit the Noctua at th top of the heatsink, no need for it to be a slim one.
You can't attach a 3rd fan to the Fuma 2 in the NR200. In the normal position (exhaust) the heatsink it's too close to the rear of the case and in this position (intake) the 24-pin cable gets in the way. At most you'd maybe be able to ghetto-mount a smaller slim fan, which would probably not be worth it.