Reinstall the system fresh, that is way less trouble. The games from the HDD still work. For the saves you just need to create the accounts in the same order (including deleted ones) so the internal user id lines up, so the saves are recognized
Make sure it's really running the redNAND. Did you check the size in the system settings?
Could be that your SD is failing...
You could dump and share your logs
For installing ISFShax, any SD card should work. Only PTB has the restriction that it needs a 2GB or smaller card, but if it doesn't get worse, you won't need PTB.
For redNAND I recommend a endurance card from a good brand like samsung or sandisk