Okay, redone ability scores:
+2 Strength, +2 Dexterity, +4 Constitution, +6 Wisdom, +6 Intelligence, +4 Charisma.
The languages thing was part of the TARDIS, but was reliant on the Doctor. I think it's best to describe it as being a Universal Translator type ability which works on the TARDIS and Doctor both being simultaneously healthy. Along with that, we have a TARDIS and Time Lord Prestige/Advanced class to implement.
I'm leaning towards a Dedicated Hero and/or Smart Hero progression path towards becoming a Time Lord...
Time Lord
HD: d8
Will: Good
Fort: Good
Ref: Good
BAB: As Rogue/Cleric
Defence Bonus: As Investigator
Reputation Bonus: As Investigator
Requirements:
Race/Species: Gallifreyan
Skills: Computer Use 9 ranks, Knowledge (History) 9 ranks
Feats: TARDIS Training* (the effects of this feat are that you can use a computer use check with a TARDIS as an attempt to use it)
Features:
1: TARDIS Familiarity +2, TARDIS Psychic Link
2: Improved Regeneration +1
3: Lesser Time Manipulation
4: TARDIS Familiarity +4, Body Manipulation
5: Improved Regeneration +2
6: Medium Time Manipulation
7: TARDIS Familiarity +6
8: Improved Regeneration +3, Greater Body Manipulation
9: Greater Time Manipulation
10: Time Immunity
TARDIS Familiarity (Ex):
The Time Lord gains the indicated bonuses to use of a TARDIS at the indicated levels.
TARDIS Psychic Link (Su):
A Time Lord is psychically bound to his TARDIS. Upon a critical hit, damage can be transferred instead from the Time Lord to the TARDIS itself upon a successful will save with the DC being equal to 5 plus the damage rolled.
Improved Regeneration (Ex):
The Time Lord gains the indicated bonus to saving throws when undergoing regeneration.
Time Manipulation (Sp):
Lesser: The Time Lord gains the ability to increase his speed, as per the Haste ability 1/hour
Medium: The Time Lord's lesser manipulation increases to 2/hour, and he also gains the ability to slow down every enemy in an immediate 10ft radius 1/day
Greater: The Time Lord's medium ability increases to 2/day, and lesser ability increases to 4/hour. The Time Lord also gains the ability to freeze time, as per the Time Stop spell.
Body Manipulation (Ex):
Starting at level 4, a Time Lord can stop his metabolic functions and enter stasis once per day for up to an hour.
Improved Body Manipulation (Ex):
Starting at level 8, a Time Lord can effectively cast 'regeneration' (as per the spell) upon himself once per day.
Time Immunity (Ex):
The Time Lord becomes effectively immune to an earlier self being killed, as his current self is welded almost entirely to the Time Vortex, and cannot be killed in his past but only in his present.