Here is an excellent resource created by one of the users here. It discusses many aspects of clipping that can occur in the Pod HDs. Thanks go to meambobbo.
I read that and tried everything it mentioned in regards to input output and gain staging, and I lookd up many other users who have had similar issues to me.
The only progress I've made so far is when I turn down the treble knob on the amp, or the tone knob on my guitar, I can reduce the amount of clipping, in fact with the treble knob all the way off the clipping is gone, but in both cases the tone is unusable.
I also tried various ways of reducing the input level, such as turning down gain, master, input impedance, input sources, guitar volume and tone, bias levels, channel volume, you name it, all of these will have very little effect on the amount of clipping.
I can get the input level to be so low that even with the physical master volume knob cranked I can barely hear the sound, it would still be clippd to hell.
I tried setting the pod to tuner mode and my guitar volume to barely audible, still clippin...
But I did notice that it clips way easier on the lower bass strings and not as much on the treble strings.
At this point I'm almost 100% sure I'm not clipping the pod, I think it may be the EMGs preamp clipping.
Does anyone know if a 18v mod may alleviate this or if there is something else I can do? I have both pickups already fairly far from the strings.