The Clear-PEM detector is a positron emission mammography scanner based on a high-granularity avalanche photodiode readout with 12 288 channels. The front-end sub-system is instrumented with low-noise 192:2 channel amplifier-multiplexer ASICs and free-running sampling ADCs. The off-detector trigger, implemented in a FPGA based architecture, computes the pulses amplitude and timing required for coincidence validation from the front-end data streams. A high-level C++ simulation tool was developed for data acquisition performance analysis and validated at bit-level against FPGA VHDL testbenches. In this work, simulation studies concerning the performance of the on-line/off-line energy and time extraction algorithms and the foreseen detector energy and time resolution are presented. Time calibration and trigger efficiency are also discussed