Like I said, I don't have the Mod 50, but you can see modular thinking in the Tourmaster design- It basically has four modules, but you can't remove them.
On the whole I have found the Egnater complicated. I like that, but it did take some getting used to. I find that I am constantly re-eqing and re-setting it depending on what guitar I am playing, playing conditions, etc...
Most amps you can just set everything at 12 o'clock, plug in pretty much anything, and go. The Eggie doesn't work like that. I got used to this amp using Egnater's recommended settings, virtually all of which have boosted bass and treble and cut mids in some form or other, at least for the Tourmaster. Now I am clearer on fooling around with it, but those presets were really useful to get a hold of this thing initially.
Many of the clean channel settings keep the gain low and crank the channel volume- Not what you would always think to do.
In the end, I had to adjust my thinking to the amp a bit, and that took some time.
For the low gain settings, I either don't use them, or I tweak them a bit, or mike them up, or use them only for recording, or when they are appropriate to the situation.
It's worth remembering that many Egnater amps are really flexible, and that can actually take some getting used to. There's some different thinking behind these things.
So- Maybe there is something wrong with your amp, but are you certain? Does the Mod 50 have some suggested pre-sets you could try and fool around with more? Maybe you need to adjust to the amp more?
Many people do experiment with different pre-amp and power tubes, and that may produce something more to your liking, but it doesn't mean that there is something wrong.
I tend to think that, when confronted with a problem, guitar players- me included- often tend to look at adding and complexifying to solve it, when maybe we should look at subtracting and simplifying. I have often solved problems by getting rid of something rather than adding.
Food for thought. Hope you resolve this!