I'm not talking about mixing. I'm only talking about recording. One way to check that the recorded audio is clipped or not is to look at it. Clipped audio will look flat where it should have a smooth parabola looking top and bottom.
Your levels for recording are dictated by the very loudest sound you record. If that is not clipping nothing else will.
I am not that worried about the signal going into the red. Its clipping that is of great concern. Clipping means it is louder then the A/D converter can handle and will simply cut off the top. Its that cutting off the top that can sound bad.
I did listen to your sample and it very well could be due to clipping but I'm not sure.
I get the feeling that you are not understanding what I am telling you about setting up for recording.
This is very important. If you set the record track fader at any value other then zero you will not get a true reading of what is streamed to disk. Adjusting it while recording will not change the level going to disk only what you see and hear if you are monitoring. It will look like you are lowering the level when you are not. That has to be done at the signal source.