I thought you put the air filter on the throttle body (with a couple of couplers and MAF) compared to using a tube and filter
This was mentioned earlier in this thread but the basic fact is this:
The first test you ran richer than the second...If you had more hot air coming in and your car leaned itself out more and is probably why the car gained power.
So basically....If you would have just left the box on and leaned your car out a little you would have gained the same amount of power.