This paper demonstrates the importance of parameter initialization in the co-simulation of integrated circuit emission in a Transverse Electro Magnetic (TEM) cell using the time windowing waveform relaxation (WR) method. The study focuses on the Freescale MPC5534-324 microcontroller and uses an equivalent circuit-based model for the TEM cell. The WR method is applied to three subsystems: the power distribution network model, the Integrated Circuit Emission Model (Conducted Emission), and the far-field coupling model to the TEM cell. Initially, WR parameters are set to zero, and with a 1.8 V input, the co-simulation output shows an average error of -16.4 dB compared to the full system, requiring 9 iterations and 14.45 s of CPU time -33.8% slower than the full system. Accuracy is improved by using WR output values as initial parameters for the time windowing WR method. With 14 iterations across four time windows, the average error improves to -45 dB (less than 2% difference) while reducing CPU time by 32.2% compared to the basic WR method. These results underscore the critical role of informed initialization in achieving accurate and stability in co-simulation.