We get these bubble level type app for phones and mobile devices. They all have a calibrate option. If you place the device on a surface that is not level and choose to calibrate the device, your bubble level is always going to be inaccurate. This is similar to your using mp3's to calibrate your setup because your reference, the source media, is already altered from the original. Don't ever use mp3's to calibrate any sound setup. setup. Similarly, cutting off the sound at 40 Hz, is fundamentally limiting your setup. That subwoofer if placed in a corner, will definitely produce usable output down to 20 Hz.
I'm sorry to say your knowledge of how to correctly setup the system needs to be bolstered with a lot of reading and learning. The AV University section here has tons of good articles.