My 2 cents..
SRD quote from above. " It retains any class abilities, feats, or skill ranks it formerly possessed. Its class, base attack bonus, base save bonuses, and hit points are unchanged. "
It does not mention anything about Racial abilities, feats, skill ranks, BAB, etc...
Here is my take on it:
The spell creates/summons/whatever new body for the target of the spell.
Lose 1 level, or 1 HD if no levels or 2 CON points if at 1 level/HD.
Remove all racial stat modifiers based on the old form.
Remove all racial abilities based on the old form, including racial HD.
Adjust the HPs due to change in CON/HD
Leave any cultural ablities based on the old form, such as the Human bonus feat and Elvish weapon proficiencies.
Add all racial stat modifiers based on the new form
Add all racial abilities based on the new form. You do not gain skill points or cultural abilities.
Roll any added racial HD and adjust HPs based on the new CON score.
Add any LA based on the new body
Ideally, the table should reflect only +0 or +1 LA different from the target creature. The 'win' of gaining a 'better' body is offset by gaining the LA. I would not think it would be broken to allow even a +3 LA on the table, as the XP spent to catch up can be described as the character taking time to adjust to a radically different body.
I agree that this one is not very well defined.. but IME the use of the spell is not that common.
An interesting thought that struck me as I wrote this.. using Sean Reynolds 'lycanthropic as class levels' rules, a reincarnated lycanthrope would retain the disease!
I guess as long as you define the disease as a spiritual/soul disease instead of a physical one....hmm, interesting. Now I feel like using a 3.0 table and getting a Were-Rat Bugbear!
Heres an idea.. would anyone be willing to submit thier idea for alternate tables for different races?