Interesting. Alter Self unambiguously gives racial skill bonuses, but might not give the special quality Blood Quickening, which gives you the racial bonus in the first place.
Ultimately it boils down to whether you believe Blood Quickening is Ex or Su. If it's Ex, then Alter Self grants it. If it's Su, then it doesn't. The sample Spellscale NPCs in the book are printed with the new statblock that doesn't specify whether a special quality is Ex, Sp, or Su, so we can't tell for certain. It's a DM's call.
Interestingly, Alter Self also grants racial bonus feats, so you'd probably get whatever feat is tied to your Blood Quickening choice as well.
Personally, I tend to rule in favor of the player if something is ambiguous, so I'd say that it works. However, activating Blood Quickening takes an hour, and I'd rule that time spent meditating counts against the duration of the spell, so they'd have to be at least 7th level to get any benefit out of it.