UPDATE
I checked out your settings here using Sony MDR 7506 headphones with a Hamer Special
and I did a signal strength test on the bench. Here are my conclusions:
I do hear and see (on the scope) the soft clipping on initial string attack and decay you experienced. This is tube stage clipping in the first two gain stages, putting it before the FX Send as you described.
At the settings you posted, this is normal. For reference, turn the preamp volume of any guitar amp you have up to around 10:00 and you will likely get a similar distortion, especially with humbuckers. On some amps, non-MV amps in particular, the volume will be loud enough that you will be forced to back off on string attack as it will be quite loud and your natural tendency is to avoid pain. With an amp like the GPDI, you have the ability to lay into it without worrying about volume or ear damage. But that will also allow you to hear the subtle distortion artifacts you normally don’t experience at volume.
To reduce this distortion, do the following -
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Turn Gain I down to 8:00 to 9:00 max. For reference, most Blackface Fender style amps start distorting at 3 or less on the channel volume, which is equivalent to 8:00 to 9:00 on the clock face.
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Set the voicing switch to the Clean setting. The Deliverance and Pittbull voicings will add a little grit to the sound and bump up the mid gain a bit, which is intentional. As Gain 1 increases, we want a gradual onset of overdrive as you roll into higher gain settings. If you want more brightness on the clean sounds, turn up the Treble and back off on the Middle to around 10:00-11:00.
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Turn the Master volume up. In my test, I set it as high as 1:00 - just at the threshold of power amp clipping with Gain I at 9:00 (NOTE This clipping threshold goes DOWN as gain goes UP). Getting a little power amp mojo happening will help smooth out distortion artifacts in the clean sound. This is why even though Fender amps are described as “clean” they are also quite distorted if you listen closely when you pass 3. Again, these artifacts get masked out at volume because the power amp and speaker behavior are acting as a filter. Your ears are also trying to filter out distortion at volume, a known phenomenon that doesn’t happen with the GPDI unless your headphones are cranked.
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Set the Dynamics control to zero. This will provide maximum plate voltage to the preamp tubes and therefore maximum headroom. On the other hand, the overdrive harmonics will soften at the onset of sag, so increasing the Dynamics setting may also work for you.
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Experiment with different IRs. The one selected in your photo above - 3/1 - is the Fane loaded Deliverance 412 cab mic’d with two SM57s. It has a lot of top end detail and is fairly tight on the low end. A better choice would be 1/3, the Sound City 412 with the same speakers but a more open low end and is mic’d with an SM57 and a Royer 121.
Hope that helps!
Dave