Matching the stiffness of the structure you are replacing, or, at least not negatively impacting it, preserves the existing response. Computationally this is pretty trivial to calculate even by hand so I don't see that as an issue, and I am thinking in 2005 terms for software tools.
The easiest way to avoid a structural resonance with one of the N/rev frequencies is to have your engineers design the structure to hit it. In my experience, including through 2005, is that it is not that easy!
To what degree does the fuse skin on the Blackhawk transmit loads?
The Blackhawk structure is very conventional semi-monocoque construction. The skin definitely transmits loads, especially in the tailcone.