6. Your mass numbers for the structure look pretty good. Have you considered varying the live load applied to the structure? NIST and some researchers, such as Purdue, use a relatively low figure as you do here, but there are others such as Dr. Quintiere who suppose the live load was up to three times as high. There is some support for either argument, and it is also suggested that NIST's live load refers only to accessible flammable materials rather than actual mass. I accept your assumption here as reasonable, but it's a parameter that remains largely unknown and has the potential to affect your results, so you may want to make it controllable as well.
The live loads in the spreadsheet are set to the maximum rated loads for all floors, and are also specified separately for the inner core and outside core areas.
(MAXIMUM Live Load as per ASCE 7-02 as applied to original design specification for WTC. NISTNCSTAR1-2A P102)
I feel that without further definite data, that the usage of the maximum design rated load is more than reasonable, however, as the data is housed in a spreadsheet, the loads can easily be changed by the user on a per-floor basis. (Sheet Tower Mass, Columns P thru V)