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I don't have access to any softwares so I don't know about your framing. But, for Steel Design, don't model 2D unless you are completely familiar with the overall process. Generally, steel columns(I shapes) can be moment connected in the major axis and braced in the minor axis to provide a load path for lateral loads. You should see what you column orientation is. Unlike concrete, for steel design, you have be watch the load path. Engage a senior engineer in your office and get him to review what you are doing.

W4x13 column looks thin and light. I can't open your model as don't have Etabs with myself but I wouldn't use any thing less than W12 or W14 for columns. Section should be bit heavy too as heavier sections help in connection design. The checks you need to perform are member beam column utilization checks. Normally programs call such checks as unity checks and show unity ratio. There is a watch and learn video on Csi webpage that shows you how to select a section list and let Etabs select members that would satisfy drift requirements. Rana has made some good points too.

12 Modes are very few and I believe is the default number in settings. You should run your modal analysis for at least 300 modes or 95% of Static Dead. Check your magnitudes for cases of Turbine Operating and Generator Operating and superimpose them to see if the total doesn't exceed vendor limit at points specified by vendor. Since your operating frequencies are different for both turbine and generator, you should have two files for each case operating with pile impedances referring to the speed of forcing function. Regarding Modal Analysis, You have to see two bandwidths. First one is from 0.8-1.2 of your Generator Operating Speed; which would be 20 Hz to 30Hz and the second bandwidth will be from 0.8-1.2 of Turbine Operating Speed. For each case, note all the modes that fall into the bandwidth. Then run Modal Time History Function by equating your forcing function to the frequency of the mode(that's how you check resonance). Superimpose the results for each operating case and if they are below the vendor allowable limit at the points vendor has specified. you are good. Thanks.

You need DYNA5 to get pile impedance(stiffness + damping) values. DYNA5 would calculate these values for your pile group considering group effects. You should convert the group values to single pile, and use them in SAP2000 as a One Node/Joint link and do the Modal Time History Analysis. Find your critical modes and check structure for resonance. If your amplitudes are lower than vendor allowable, you are good. Tell you company to buy DYNA5.