I have had this happen to me before. I didn't have the OG charger and had to leave it charging for almost 48 hours to get my PC to recognize it in RCM mode. Hopefully it just needs more time. Good luck!
You need the the rxtools folder with rxtools.3dsx in it from the ninjhax folder in the rxtools archive. Put that in your 3ds folder on your sd. That will make rxtools available to boot from hbl
Yes you should have boot.3dsx also. Did you install menuhax in emunand? Try deleting both payloads. Then change themes in sysnand and emunand. follow the coldboot guide again and change autoboot to 10 in boot.cfg