The build looks absolutely amazing; the cable management looks superb, better then the state most so called "professional" builds come in. This next part here is just me nitpicking so feel free to ignore it completely if you like; this is just for aesthetic purpose and won't affect your PC performance in any real way.
Anyway now on to more real matters.
The reason why your temp went up is because before you had air blowing right on your heatsink but now that you made the top fans exhaust, you lost that air. Don't get me wrong though, the top fans are usually meant to be exhaust so the real issue is with the overall airflow in the case atm. You now have more exhaust fans in your case then intake and not to mention the only intake fans you have are further away from the CPU heatsink. Also your 2 140mm aftermarket fans on top are probably better quality then the 2 120mm stock fans on the front; this situation is creating an uneven airflow and since the heatsink is not high end, the overall cooling suffers. This is partially my fault, at the time i recommend that specific cpu cooler, it was under the assumption that it was to be used in your old dell case. I apologize for that, i would of recommended something else all together if i knew we would be using a better case.
The best option now is to probably get 2 more 140mm fans and attach it to the side panel as intake fans; this will blow cool air on both your cpu heatsink and gpu. If your using the molex connector to power your front 2 fans, then you should still have 2 more 3/4pin inputs left on the spliter. If you don't then try to buy fans that come with the adapter cable, Nzxt fans tend to come with the 3pin to molex with each fan. You can also attach one at the bottom beside the PSU but i think you will benefit more by attaching to the side panels.
Also for the FP1 input, good to hear the power switch works; for the LED i figured those were for LEDs but i was guessing as to which is which LED. Make sure the power LED on the case is always solid and not blinking, if its blinking then you probably have it in the HDD LED input. If both LEDs are working then all good but if only one is, then the 2nd is probably the pins labeled as "Reset Switch". Feel free to play around with it a bit "If" its not working as intended, no harm long as you know where + and - are.
Congratz on getting your build up and running, it really looks amazing^^, makes me want to do upgrades on my own build lol.