How about just creating a preset and playing guitar instead of a CD? How about a really clean amp (twin would be good - bright off), cab and some reverb -- without any advanced EQ tweaks or blocks.
If you do not find that bass heavy -- great. Everybody has different tastes.
If you have to start knocking down EQ bands to normalize the cab for guitar then would you agree that the cab was a little bass heavy to begin with?
Not saying that is a bad thing. For some styles of music that is actually a major benefit.
When the kids borrow my car they bump up the bass in the stereo because that is what they are use to hearing -- drives me crazy to say the least.
From everything I've read of your comments, it seems you are coming at it from wanting a live amp sound and feel.... Which is totally cool... There's no right or wrong, only what's right for YOU.
If you create a tone on a real Fender Twin, and EQ it to your taste, it will sound just like you like it in the room. Now, if you bring that same amp into me in a big studio to record it, I'm going to listen to it in the context of the band... With bass, drums, and vocals, it's entirely possible, that the level of low end in your tone, while it may sound perfect for you, may be too much to fit in with the bass and the kick... The live world and recording world, may require different EQ.
Here's where, it seems, your ideal tone, the CLR differ. In real amp and speaker ( such as a Celestion Vintage 30), the frequency response is listed as 70-5000hz, so there is not much frequency information above ~5000hz, or much below 70... It is naturally rolled off, because the speaker is not a full range speaker. So, in a FRFR speaker, such as the CLR, which is designed to reproduce more of the full audible frequency range, you may have to roll off the frequencies above 5k and below 70hz to get it to sound "natural" to your ears. If you are trying to MIMIC. (. ;-). ) a real amp, you need to limit the frequency range going to your FRFR.
The problem, is that the AxeFX II is ABLE to create frequency information across the full frequency spectrum... As in the synth patches...
Even though you do these things, it *may not* sound like a natural amp to YOUR ears, and that's ok too.. It just means that what works best for YOU, might be a real power amp and cab... To each his own.. There's no right and wrong, only what works best for each person...