I was wondering if your simulation was for an actual engine or as you say, "a dummy engine?" It might be helpful if you could move on from the dummy engine to an actual engine you can compare your simulation model to. Both the simulation model you referenced here and the one I just added use actual engines to compare their models to. The paper I added deals with contrasts between the model and engine in more depth then your reference and I believe it is a bit more specific and maybe even precise.
Being you're a student I think suggestions at this point are appropriate for identifying, defining and correcting for losses in your model. Again get an actual engine to apply you model to. If you don't your model and coinciding paper will come down to, "I did this because. . . .I think based on. . . ," which probably won't carry as much authority as working with actual deviations between your model and an engine will. If you don't have access to actual data ask for permission to use someone else's. I don't think you'll have much difficulty getting it.
For methodology I would pursue comparison and contrasting. Overlay the actual engine graphs with the simulation and where they match, define why. Where they don't match pursue reasons why they contrast. Document the process for your paper even when you get it wrong because "the wrong," should show up somewhere in your simulation and hopefully you can, or with help from here you can present the effects of your pursuit and explain the error. In the papers you have there are their, "we were wrongs."
I'm not speaking for anyone else and their thoughts or input but I can suggest a couple of places to start.
The compression ratio stated for an engine is usually the "Static" ratio. It's what you use in your model arguments. The compression stroke is presented as BDC to TDC. The intake valve doesn't close until after BDC though. This is the "Dynamic" ratio which is always lower then "Static" ratios. There is no formula for converting cylinder pressure to compression ratio or vice versa. What effect does that have on cylinder pressure in your model?
Maybe Chris can help you with this since I believe this graph is his. What is going on in every other trough in the V8? Why the little skip with this pattern? Jason, how does this torque curve compare to yours?
Chris, have you ever seen a simulation that actually factored in or out, the flywheel? Or further yet, factoring for engine balances? I'm thinking of:
https://en.wikipedia.org/wiki/Engine_balance