Sorry for the radio silence the past few days- I replaced the motherboard in the 3DS, and it turned out it was exactly the issue- something was up with the NAND chip I guess, since the new motherboard doesn't even freak out when trying to start it up. It just starts up as normal. I'd probably have to hack it again, but as far as I'm concerned, the issue that was plaguing this 3DS has been cleared up.
Thanks again, everyone, for guiding me and helping me through this journey.