Yeah sorry, you said 8.4 in post #1.
I think the update back to 8.4 via your nand.bin backup might be safer than using smash brothers cart update.
It would just be interesting to see if the boot speed problem is real or if you just imagined it was much faster with the original 8.4 firmware.
True, again could be terribly wrong, but the fact that a launch 3DS boots faster to 4.5 realNAND by a clear 10 seconds might imply there is an underlying issue somewhere.