Sorry, I meant to answer both the questions at once
Schmidt - IF your acceleration data includes information at all the frequencies of interest then you CAN take the frequency spectrum of each, and divide one by the other to give a valid transfer function. In an ideal linear system the response at a given frequency is at a constant ratio for two points, always, if there is only one forcing function.
Proof: at a frequency x1/F3 =k1, x2/F3=k2, hence x1/x2=k1/k2, which is a constant
where k's are complex constants in a linear system.
The names often given to this in modal software is running modes, or operational deflection shapes.
Cheers
Greg Locock