Instrument amps aren't clean like hifi. Even playing a 'clean tone' they're still changing the sound in some way:
* pre tube stages change the tone and add harmonics, most have some form of large signal compression due to the power rail 'droop'
* power tube stages operate at full, providing extra harmonics and often with a large signal add compression due to larger power rail droop
* the output transformer at saturation will impart some sound, with single ended adding a warm second harmonic but the normal push-pull for power causing a cancellation of some even but adding odd harmonics. With proper tube amps, the tubes see the speaker load through the transformer and so changing the speaker changes the load on the output power tubes - changing the sound.
* the speaker changes the tones - these are a subject to themselves, as the material, the notes, the spider support etc all impart sound changes. If you run small speakers you're going to get a very different sound to a large speaker, but it's all about trade offs - what works and does it for you.. won't for someone else. Some people hate metal cones (fast accurate but impart high end frequency) but prefer the softer tone of paper and large for shifting air.
* the feedback (negative normally) changes the response etc
* the cabinet the speakers sit in can change the frequency response, the defraction of multiple speakers is an aberration for example that needs careful planning and trade off.
* finally the instrument and the pedals
* all of the above can modify the frequency response (ie low to high string and what comes out may be attenuated or boosted without even using the tone controls or EQ), and it's all inter-related
The issue is the subject is soo large, that people spend fortunes tracking down the precise gear to sound like Eddie Van Halen or other famous bands. A modelling amp or a modelling amp program will get you 60-75% there but that last 25% is where it becomes an obsession. Start somewhere and don't get stuck in analysis, then iterate towards your goal and stop before it becomes and obsession
So far I've only built my own tube amps, digital stuff and built small speakers but from that I've learn that there's way more than I could master in a lifetime.
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