Not completely off base actually. If the CUSE7 amp issue is anything like the CUSE8 (sure sounds like it is), they might have been talking about removing / replacing the tour pack amp, not adding to it. When you disconnect the amp from under the tour pack, it does affect the iPod and hand controls related to the head unit. This is unique to the CUSE8, and sounds like the CUSE7 as well.
If you're simply adding an amp in the fairing to power the fronts and keeping the tour pack amp plugged in, everything should work great!
I made my TP detachable. This displaced the amp into my saddle bag. I want the amp out of my saddle bag to be replaced by an Arc Audio amp in the fairing, where things should be to begin with. On the CUSE8, this is not possible without a custom harness, which I discovered during a very frustrating weekend installing the system. Turns out, the harness provided by Arc Amp will not work for this specific model. Been working with Brad at Arc Audio and Pete at Soundz Customz regarding this issue over the past few weeks. Pete is now making a custom harness so I can remove the factory amp completely, stuff a 4-channel in the batwing fairing, upgrade the speakers all the way around, and be done with this.
Also, I can confirm that you won't need to remove the tank. You can unbolt the rear of the tank, tilt it up, and fish the power/ground leads up the right side of tank in the wire well, behind the front right tank bolt, and direct into the fairing where the rest of the harness goes into it. It will look factory.
Also confirming your suspicion, finding a new home for the XM and iPod modules inside the fairing is the toughest, most time consuming part. My CB module now proudly sits atop a wooden shelf in my garage - no room in the fairing, and it will never be used.