When you say "plugged into an amp for better volume control" when recording DIs, are you running into the amp, and then from the headphone out or something, and then running it into an amp VST? If so, don't. :lol:
There's a lot of questions I have here, but one possible culprit if you're talking about volume control is, how hot are you recording your DI? Where are your peaks hitting, are you trying to boost it up to a "hotter" level somehow wither with the scarlett preamp or internal processing in your DAW? Just a guess, but it's possible you're getting "muffled and overly digital" guitar sounds because you're just absolutely over-saturating the virtual amp by feeding it a signal hotter than it's designed to work with.
As a good safe starting point, try recording a DI with no additional boosting anywhere in the signal chain, not at the Scarlett, not within your DAW, as if you were plugging your gutiar straight into the virtual amp, and see if that helps. There's a LOT else that could be at fault here, including a bad amp sim, bad cab IR, or both... but that's a possible culprit to rule out, up front.
