Hi
I would suggest that the best approch a multi frequency input problem is to generate a PSD input for your model from your experimental data. PSD is better than accleration as it is a normalised energy input across the frequency range rather than acclerations at specific frequencies.
To...
A good basic vibration book is "Mechanical Vibrations" by J.P. Den Hartog, ISBN 0-486-64785-4. It is an extreamly old book but does provide a starting point for vibration fundermentals and it has chapter covering rotating machinery vibration.
I personaly have not found a good book...