I have given the Skill respec a lot of thought and I belive I have come up with a solution. At 5000 favor you should be allowed to rebuild your character from the ground up. Since this would be a reward and not a system available to everyone the normal problems with skill respec could be ignored. here is the way I see it.
1. rebuild at 32 points for abilities (Ability to change alignment could be here as well)
2. Add what ever tomes have been read to the stats.
3. Rebuild each class level as you see fit basicly releveling.
This would solve several complaints about alignment, 1750 favor for 28 point builds, skill respec, and multiclassing. The first complaint I see to this plan is that you will wind up with more skill points than you could of had because of tomes and changeing ability scores. But thats the point. It is a reward. I envision this as a 6 million dollar man type reward. We can rebuild him. Make him stronger, faster, more skilled than ordinary characters. This is the kind of grand reward I expect from 5000 favor and this would solve a lot of problems that people have with their head start characters.
Jost a thought Let me know what you think.