my phone messed up

im new to all this.

im S-Off, and semi root, SuperSU doesn't really give half of my apps root acces for some reason.

i want to do a full reset to the phone (Return to 100% Stock)
i want just to clean it all out (which factor reset doesn't do that)
and update my softer from lolipop 5.0 to 5.1

i got HTC__621 (twiwan version)
software number 1.32.709.14

how to do all this? what i need to do?
(to flashout new TWRP2.8.7.0? then superSU 2.49 beta from the beginning?
and if i want to install Viper ROM, i need to do that after all?)

i hope to get explanation cuz i got lost on all the words (OTA - which i dont know yet lol, CID etc etc)
i got like 10 pages of guides open and yet i dont know what to do or what steps to follow.