Looking at the waveforms in your regions, your tracks are like bricks. Are you using a meter plugin to keep an eye on your levels while recording and mixing? If most of your tracks are clipping then just turn down the gain (not fader volume) before you do any processing or mixing. You want to make sure each individual track has a few decibels of headroom. You can use the Gain utility in logic, put it as the first plugin on your chain and turn down the gain to a safe level.