Yes, Fly allows both its CL bonus and your racial bonus to stack. In fact, if you don't have one, Fly gives you a 'good' (+4) maneuverability bonus in addition to 1/2 CL.
The subject can fly at a speed of 60 feet (or 40 feet if it wears medium or heavy armor, or if it carries a medium or heavy load). It can ascend at half speed and descend at double speed, and its maneuverability is good.
From the Common Terms section on Bonuses,
The important aspect of bonus types is that two bonuses of the same type don’t generally stack. With the exception of dodge bonuses, most circumstance bonuses, and racial bonuses, only the better bonus of a given type works. Bonuses without a type always stack, unless they are from the same source.
In your example, having the Fly spell cast would grant you a 60ft fly speed (if greater than your existing fly speed) with perfect (+8 racial) maneuverability and 1/2 CL untyped bonus, stacking. You would use your perfect maneuverability over the good maneuverability provided by the Fly spell, and the greater of 60ft or your base speed movement rate. You aren't casting Fly twice, so you're not comparing the bonuses from a same source.