The impact of thermal compression bonding (TCB) process parameters on interconnect quality and stress distribution is difficult to predict without trial-and-error experiments. Our work demonstrates a framework to perform an end-to-end calculation of the temperature distribution and resultant residual stresses obtained after bond and assembly of a 3D die stack. Thermal compression bonding (TCB) has enabled bond and assembly of 3D die stacks with fine pitch interconnects with minimal defects caused due to die and laminate warpage. However, the effect of TCB process parameters on the temperature distribution during bonding and residual stresses after bonding in 3D die stacked structures is not well understood. This paper focuses on understanding the temperature distribution and stress evolution during the bonding process using a validated finite-element model, and optimizing the process parameters for a 3D test vehicle. In this work, finite element (FE) thermal-mechanical modeling is performed to simulate the TCB process of a 3D test vehicle. The test vehicle consists of a 6.38mmx3.7mm full thickness silicon die bonded to a 10.02mmx7.34mmx0.1mm interposer, followed by bonding to a 21mmx21mm laminate. Our FE model includes TCB tool components such as the TCB heaters, nozzle and pedestal in order to accurately apply process parameters as boundary conditions. The thermal contact resistances (TCRs) at different mating interfaces in the TCB stack are calibrated using inferred temperatures from melt trigger signals in the TCB process profile. Using the calibrated TCRs and using our Baseline recipe for both bottom die-substrate and top die-bottom die processes, we observe significant temperature drops from the bond head heater to the C4 bumps, as well as from the center to the corner C4 bump. This high temperature difference between the heater and solder shows that the TCB process needs to be carefully optimized to ensure complete melting of solder. The effect of varying the bond stage temperature is also studied, which can enable solder melting at lower bond head temperatures. The temperatures from the thermal model are transferred to a structural model to obtain the post-bonding warpage after cooling down to room temperature.