
LonePaladin |

Which leads back to my question about the Faceless One. His stats seem to imply that he is a member of a race that affects his CR. Why is he CR6?
That Intelligence score IS rather high. Without some sort of magic (like wishes, or a tome of clear thought +2), he shouldn't have such a high stat, unless he started with one higher than normally possible. If you have a problem with it, here's how you can fix it without drastically changing things.

Are |

Looking at him, his stats are pretty special, especially considering he's a Human (according to his statblock). The elite array and the 4th level ability score increase would provide 16-14-13-12-10-8, while he has 21-16-14-14-14-10, without the aid of any items (at least not any listed items).
That said, my group didn't have any problems with him, so while his stats may be sufficient for a +1 CR increase, I don't think it's necessary

Hierophantasm |

My guess is that he was meant to have a potion of fox's cunning listed in his combat gear, with (already consumed) next to it.
His stats are a little crunchy, even with that into consideration, but this dungeon is a real, old school dungeon crawl.
So dig a wide-ol' mass grave, 'cause you're gonna be chuckin' the bodies in there in no time!

Jonathan Drain |

The reason for the faceless one's increased ability scores is that a single spellcaster NPC is actually weaker than his Challenge Rating would suggest. This is kind of an elephant in the living room, in that nobody really admits it when writing adventure because it would break the rules, but playtesting will show that it is weak. Any NPC, especially a wizard, needs ridiculous amounts of extra buffs to be anywhere near equivalent to monsters of a CR equal to its level.
There are several reasons why this is the case:
1) NPCs don't have a player's amount of magic items - if they did, killing four NPCs of your level would double your gold
2) Wizards are balanced to be protected by a cleric, fighter and rogue. Solo, they could be defensively too weak to get off more than one or two rounds of spells.
3) Wizards are balanced to use their spell selection spread across perhaps four or five encounters in one day. They simply can't make use of all their power in one fight like a monster can.
In other words, as an NPC the Faceless One is fine as he is.

Callum |

That Intelligence score IS rather high. Without some sort of magic (like wishes, or a tome of clear thought +2), he shouldn't have such a high stat, unless he started with one higher than normally possible. If you have a problem with it, here's how you can fix it without drastically changing things.
** spoiler omitted **
Alternatively, there's a cloak of charisma +2 just lying around unused in his lab! Why not morph that into a headband of intellect +2 that he's wearing?