Rather than mess with the (even flawed) CR system, let's just beef him up enough to warrant his CR.
In addition to unholy toughness, how about giving him damage reduction 15/bludgeoning and magic like a lich or death knight, immunity to cold like those two, spell resistance 13 + 1 per character level like a sketal warrior, and vampire bonus feats (Alertness, Combat Reflexes, Dodge, Improved Initiative, and Lightning Reflexes)?