The III hovers in green led territory with casual strumming and very rarely reaches red.
This is fine. You should just tickle the red with your hottest guitar while playing your hardest. Setting input levels is about maximizing signal-to-noise ratio without clipping the input. Increasing the global input level is not going to affect how hard you are pushing the virtual amps.
I do wonder if there is something else going on before the Axe-Fx, as I have set my input levels to 15% with fairly hot passive pickups, and just tickle the red when I really smash the strings.
Thanks for the input. I may be using the term "breakup" incorrectly so I've made a quick audio sample.
Thanks for the audio sample. I would normally use the work 'breakup' to describe the transition from a clean amp sound to something that has a touch of distortion. Both those clips sound about what I'd expect from those presets, and the Petrucci example is well beyond 'a little breakup'. That's OK though, it sounds like you like your amps pushed a little harder than the standard presets. Just bump up the input trim on the amp itself, or increase the gain control on the amp.
Ideally I would like to be able to switch guitars out and crank the input for lower output guitars easily AND also have more input gain on every preset without having to adjust every input block on every preset.
If you are keeping the gate settings the same on every preset, you could
link one of the input blocks to a global block, and then "Link-to and Load-from" to this global block for every preset. This will enable you to change the input gain for every preset when you change guitars. The downside to this approach is that you can't then set input gate settings specific for each preset.
Another thing to consider would be linking the
input trim parameter in the amp block to an
external switch. Then when you change to a low output guitar, just press the external switch and you get an input boost. You would still have to set this up for each individual preset, but you only need to do that once. Even better might be linking this to a volume pedal, giving you variable control over the level of input boost.
I would question whether you want to change the input gain for all presets, but that's just me.