if you want to follow the posted paper, you should define a nonlinear time history analysis. This requires a direct integration of the equations of motion ( see for reference the Wilson's book http://www.edwilson.org/book/book.htm). Follow SAP2000 manual to build up a nonlinear analysis and which kind on nonlinearities could be treated in SAP2000.
I hope you have found the answer to you problem, anyways i did the IDA in sap2000 which takes huge computational cost for 3d models. IDA in SAP2000, You can define your own nonlinearities or can apply the predefined ones on the software to your model. Then using different time histories (you can easily get from the PEER scaled according to your model time period) and input the time histories in sap2000. use the scale factor from peer file to scale the earthquake up or down according to your time period. and then perform the Direct integration timehistory analysis because other procedure will not consider hinges except pushover. Finally after geting the displacement you can get the result in excel and find drinft ratios for IDA curve (extracting data from sap2000 is quite hectic part because it does not give story drift directly you have to develop a program or do it manually) . I hope it would be helpful.
I'm also looking for information about how to use SAP 2000 to make IDA of an school building, because the PERFORM 3D isn't easy to use and, by the other side, using SAP 2000 we can process the answers ourselves.
I would like to be in contact with you about this topic. Please, contact me.