i feel like I've done the things i've read, but feel free to drop knowledge. I feel like the Axe is dulling the amp tone, for lack of a better term.
If it's sounding dull that usually means the levels are low going in to the amp or through the effects loop. I've done unity gain, 4CM setups, for top-tier pros and the difference between the unit in bypass and engaged when it's all shunts is unnoticeable. So let's work on that?
Here's the preset you're going to be working with:
It'll take some time to do this so make sure you've given yourself time so you can work through it patiently.
Setup up the first part of the 4CM chain: guitar -> Axe-Fx II -> output 2 left -> input of the amp. Nothing in the effects loop of the amp for now. First make sure the input signal for your guitar is setup so that the input lights tickle the red from time to time. You're a veteran AFII user so I'm sure you know what I'm talking about here. Under the I/O menu make sure Output 2 Echo is set to NONE.
Now, with the Output 2 Left running in to the front of the amp, adjust the Output 2 level knob on the front of the hardware until there's no difference in volume between when you run your guitar in to the amp vs. when it's running through the Axe-Fx II and in to the amp.
Once you've got that first gain stage setup we'll move on to the loop.
Setup the second part of the 4CM chain: amp FX send -> input 2, output 1 left -> FX return. If the effects loop is parallel set the mix to 100% wet. If it's series, nothing to worry about.
Now, just like before, you're going to make sure that the signal going through the 4CM setup is as loud as the signal when it's just guitar -> amp. This time you're adjust the Output 1 knob though.
When you've got it equal you're at unity gain.
Head to the UTILITY menu and page over to the VU tab. Write down the values you see for OUT1 LEVEL and OUT2 LEVEL on this screen. Tape them to the front of your unit. If you bump the knobs you can use this screen to get back to the precise values you need to keep a unity gain signal running through the setup.
When all that is done you can start dropping your effects in. Engage and bypass them to compare the signal chain with and without them in place so you can maintain that unity gain signal where desired.
Let me know how it goes!