Before we get into the samples, there are some things in the template I just realized need to be fixed. Since the HD is no longer HD+3, the feats are not original feats +1. I'm also not so sure about skills. What if we do this?
Skills: Recalculate the gem eye's skill ranks based on its new HD and Int and assign new skill ranks. The class skills of the base creature are class skills for the gem eye.
Feats: Reassign feats according to the new HD of the gem eye. Use the base creature's feats first, then add more feats if necessary. Gem eyes usually gain Skill Focus (Concentration) and Combat Casting as their first two additional feats.
Edit: Or maybe it is better to assign skills and feats as if a generic undead.
Skills: The gem eye has HD+3 skill ranks, which are split evenly between Spot and Listen.
Feats: Gem eyes have the following feats, gained in this order as they gain HD: Skill Focus (Concentration), Combat Casting, Ability Focus (Spells), Weapon Focus (claw), Alertness, Great Fortitude, and Lightning Reflexes.
Also, do we still want to leave the saves the same? I guess skeletons do, but that's wacky for the changing HD.