for simulation and modeling, I would advise the following books, which helped me at an advanced stage of my thesis, when I needed to make some simulations, to validate the hypothesis, which we could not perform on the test bench.
Pounder’s marine Diesel engines and gas turbines
By D. Woodyard
Diesel engine reference book
by B. Challen and R. Baranescu
Internal combustion engines
By V. Ganesan
Internal combustion engine fundamental
By J. B. Heywood
Handbook of Diesel engines
By K. Mollenhauer and H. Tschöke
Diesel Engine Transient Operation : Principles of Operation and Simulation Analysis