1- I guess your stiffness should be:
K= {(Fmax+ve)+(Fmax-ve)}/{(Dmax+ve)+(Dmax-ve)}
2- As long as stiffness degradation, Takeda should work just fine I guess. I recall I recommended using the Sivaselvan and Reinhorn work, as you could explicitly specify the extent of strength degradation, for instance HBD= 0.6 for severe degradation.
http://www.seismosoft.com/forum/topic.asp?TOPIC_ID=1821
However, I also recall that Prof. Pinho somewhere in the forum stated that FB fiber based elements implicitly capture deteriorating behavior to a good extent. I feel that there may not be a unique, conclusive answer to either only using the element only, or element + deteriorating zero length link element and say which one is more accurate. At least, it is beyond my knowledge. More experienced users could help.
I also want to address that, when you introduce a link element like smooth link element to incorporate deterioration, slip, pinching, and degradation you are explicitly specifying for the model that this will happen, which in reality may not always be the case. Keep this in mind, since I have had to deal with it as well.
3- For damage accumulation, it depends what damage measure and type you want to calculate. The response parameters you stated are straightforward. I recommend reading papers that have incorporated Park and Ang damage measure. For start you can read below papers where they used Takeda, which is the one you use, and calculating damage measures.
Park, Y. J., Ang, A. H. S., & Wen, Y. K. (1985). Seismic damage analysis of reinforced concrete buildings. Journal of Structural Engineering, 111(4), 740-757.
Van Cao, V., & Ronagh, H. R. (2014). Correlation between seismic parameters of far-fault motions and damage indices of low-rise reinforced concrete frames. Soil Dynamics and Earthquake Engineering, 66, 102-112.
Cao, V. V., & Ronagh, H. R. (2014). Reducing the potential seismic damage of reinforced concrete frames using plastic hinge relocation by FRP. Composites Part B: Engineering, 60, 688-696.
Van Cao, V., & Ronagh, H. R. (2014). Reducing the seismic damage of reinforced concrete frames using FRP confinement. Composite Structures, 118, 403-415.