Thanks for the help. I was able to think about it all day and after a bit of digging I found that I managed to miss plugging in the molex for the fan speed controller (built into the case). Now the front fans and side fan is working as well as the LEDs.
Rear fan is still MIA, found out that it's three prong plug seems to fit nowhere in particular. And unfortunately there is no manual for this case, nor can I find one anywhere online.