at the outset, i want to suggest that you DONT actually need to send .ebk file which you did in zip. .$et file is enough for anyone to review and check.
The facility is in seismic zone 4
Make LL factor in p-delta = 1.0 (im leaving the question for you to research..why)
You have made the base fixed, take care in the design of baseplates. (Bi-axial moments....how would you design it)?
Coming back to your main question, When i ran the model, all of the members passed including the columns. (LOL). Is there something I am not getting?
Check in your model, the effective length factors for columns and beams. They might need to be adjusted.
I would assert that you should have made a simple 2d model of this and should have studied it properly before starting the 3d model. Its never too late, if you haven't done one yet. You can do it now. In 2 model, check how much are the reactions, column axial forces and drifts to have a FAIR idea about the structure you are dealing with.
For drift, search in this forum. I have made a lengthy topic about building drifts. Just do the struggle to search it.
I am surprised to see no WIND load on the structure as it would be more critical for uplift of foundations and drift (If seismic is not governing). Is that the reason?
0.25inch thick shell to model the slab? I would recommend to make it as thin as possible (to the point just near where ETABS does not start giving errors...try 5mm may be). This is to exclude any out-of-plane effects of the shell.