Guess I have to ask why it wasn't possible in the FEA package, but the linear acceleration equivalent depends somewhat on the structure that is being analyzed. A flexible structure has a low "Dynamic Load Factor" where are stiff structure may have a pretty high DLF. 2 is probably conservative...that suggests an infinitely stiff structure, if I recall correctly. Usually 1.8 is pretty reasonable for strong, steel structures. You may use 1.2 to 1.4 for flexible composites.
An 11ms pulse is pretty short. There probably wouldn't be a great deal of energy imparted into the system over such a short time period...gut instinct says you're probably OK...just my opinion, though.