Exception 3.4 talks about the period, T.
It says: "The period of the entire structure shall not be greater than 1.1 times the period of the upper portion considered as a separate structure fixed at the base."
I had not seen that before as we've never performed a two stage approach (the 10:1 ratio on stiffness required to use this approach per exception 3.3 limits how often you can use it). So you would analyze the upper portion of the structure using the period for the upper. The base shears at the base of the upper would then be applied to the top of the lower times the factors designated in exception 3.2.
The lower portion analysis: For the period, would you use 1.1 times the period of the upper portion or would you use the period calculated for the lower portion system with the full building height as h??
Personally, I would model the building and use RISA to direct calculate the whole-building period, T. Then I would apply the value Cu (from table 1617.4.2) to a Ta value determined from Equation 16-39 or 16-40 to get the upper limit.