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Since you have it connected via USB there's no "volume" coming from the iPod, the radio is playing the music files directly off the device. I have an iPod Classic connected via USB to the base radio (RES? 130?) and I have no problem with the volume.
It's a long shot, but perhaps did you mess with the "volume adjustment" option for songs within iTunes? Launch iTunes, right-click on a song, select "Get Info", click the "Options" tab and look at the "Volume Adjustment" setting. Is it at "None" or is the slider moved?
I also have MP3s on a USB stick and get the same volume level as the iPod, the iPod just holds more music.
2016 Challenger R/T Scat Pack, B5, 6-speed, SPAG, WRTs, sunroof, SGII, Convenience, Tech and Leather; UPR catch can, skip-shift eliminator, Mopar splash guards.
2006 Jeep Grand Cherokee Laredo, Inferno Red, 4.7L V8
RIP 11/2/14 - 2011 Challenger R/T Classic GWE 6-speed