I have retextured my draugr although the eye effect is very unfitting. I was wondering if anyone knew where on the .nif file this effect was located. I know it is not on my draugr as a spell.

Its probably the vertex colors on or around the eyes in the mesh. That is where Shadowmere's is located. I used nifskope to change it from red to blue.

I've been scanning the mesh in nifskope and have found nothing cluing me in as to what is causing the glow effect.

Eye glows for Draugr are added by the visual effects:
FXDraugrFemaleEyeEffect
FXDraugrMaleEyeEffect

Its done by the abDraugr spell, which uses the texture 'FXDraugrMaleEyes.nif'.

I forgot to remove that abDraugr spell from my race, thanks for the help!