Wait so should i do the secure value stuff last?
(Probs a stupid question)
Did you complete everything else where all the games are loaded back on HOME Menu?
After you restored the saves with
(2b) Restore Saves and restored missing tickets with faketik, your next naturally instinct should be to mass backup all the game saves + extdata with Checkpoint or JKSM save manager.
This is to prevent accidentally losing any saves for certain games that have Secure Values. Not all games have this anti-cheat protection.
Once you've ensured all the saves + extdata have been backed up, you can remove or reset their Secure Values that are currently in place by deleting that specific NAND file found at
1:/data/<ID0>/sysdata/00010011/00000000.
Be careful to not delete anything else.
Once that file is deleted, any games that have Secure Value will not be tripped with erasing their saves the next time you launch them.
You can then mass unwrap all their icons with Cthulhu and continue back with using your 3DS as-is.