Hello! I am in the same exact situation. Let me know how things turn out for you, and I will do the same.
One thing that I did get from Mesa/Boogie related to this: be sure to get your volumes set, and all equal, with the Loop Engaged vs. Bypassed (using the mini toggle). Simple way to do this, is to connect a small patch cable in the send and return jacks. Set the Loop Level to Normal. With the loop hard bypassed, set the channel master to your desired level (with the Loop Bypassed, the front panel Output and Solo are not in use). Now engage the loop, and set the Front Output knob to match the volume of the amp with the loop bypassed. This way you know that the level of the amp is the same with the loop engaged vs. bypassed; one less variable to consider before moving onto the FX Unit.
Good luck!
JC
PS - What are your Channel 2 settings? I have not been able to really dial in that channel for a usable tone.