You are already s-off which is good
Flash a new recovery (recommend "4EXT recovery", see my signature), flash it using fastboot commands (search for guide)
Then boot into recovery, make a nandroid if you have data you need to save, you can restore it later using an app called "nandroid manager"
Then full wipe "wipe all partitions except sd card" from recovery, and flash a new rom.
(Optional) before your flash the rom, flash the optimal hboot for the rom if it has one (search the rom thread), for more efficient use of app space
Device: Nexus 5
| ROM: OmniROM
| Recovery: TWRP
Retired: HTC Desire
let's all try to get along ...but remember to search first...