I admire your enthusiasm. But I think you are traveling into a dead end there.
Those simulations are next to useless... sure, pictures are nice, but this is far away from reality.
First, airflow is not constant, its pulsating, even at manifold entry. But much more so at intake runners. Each pulse ~180į of crank rotation.
It is true that manifold acts as some kind of buffer that evens out the pulsation, but it is still not constant airflow at the manifold entry.
Second, only one cylinder sucks air from the manifold at certain point in time. There is almost no overlap on 4cyl engine.
Third, firing order is important.
Because of the above airflow patterns are completely different.
What you should do is something into this direction:
But event that has a lot of unknowns in the equation and is merely an rough approximation.
You are lacking huge amount of information here.
Now a few words about the manifold itself.
I have a feeling length of intake runners is too short.
Also low manifold volume around last intake runner will be a bottleneck.
And as a last thing to consider. JTD engines are really not limited by the intake manifold design.
Sure increasing diameter of manifold entry could help a bit, but that can be done easily by modifying stock manifold.
In short, I think you should spend your money elsewhere.