I am also stuck at installing CtrBootManager. My payload reads ".code hid:USER hid:SPVR ns:s fs:USER /bctr.3dsx APT:U APT:S APT:A gsp::Gpu srv:" in both spots and I have both the bctr.3dsx and your boot.cfg file.
Could be the latest AuReiNand build playing up maybe? It seems to be updated...