You should first design a single stage and make sure that all the circuits are operating as well as you wish, then you cascade the stages to find the 12bit ADC , in order to undrestand the operation of the pipeline ADC I strongly recommend you to simulate it once with simulink systematically.
sorry I cant download that pdf file "http://kabuki.eecs.berkeley.edu/~abo/abothesis.pdf"
can you please upload this again?
I need some paper about designing of adc pipeline (2 step flash pipeline).