I was going to setup your axis for you but you have way more issues going on and that would only complicate things further for you.
First thing is, your VE should not look like this:
Dodge VE no.jpg
They should never have peaks and valleys. They should look like a numerical representation of the engine's volumetric efficiency. This is a 1 bar but it'll give you an idea.
Dodge VE.jpg
I didn't look any further than that so I don't know if your injector data is correct but that's the first place to start. Injector data needs to be correct, all of it not just the flow rate tables.
Good luck to you.