Root Photon unique issue

Hey guys, sorry if this is a repeat, bit i cant find anyone else with this problem.
a while back i tried to root my phone a few different ways. I tried the torpedo, one click and some other way. I think i got a partial root some how cause i have access to all my root files through file manager, but no apps recognize root. There is no su binary, no busy box and no sudo is what my root checker says. Ive tried rsd lite 5.6 but there is a re-enumeration issue. I cant get back to stock. Everything works fine except normal wear and tear things. Ive tried different usb ports, i made sure the file im flashing is in the root of my c drive. Not sure what to do. Any help would be great.

Thanks in advance.