What kind of Mach Number are you trying to reach with the above intake?
I see what you're saying about the factory plenum. Wouldn't be a problem mostly for startup? Here's why I tank so: The plenum (a tank) is pressurize post startup so when the intake valve is closed on cyl 1, there will be a volume of air filling the runner, waiting to get discharged inside the cylinder. That volume will vary on RPM, cam specs, air temp, air purity (dust, oil...). When the volume gets discharged, the amount of air filling the cylinders should be fairly even.
The above is assuming the shape of the tank is uniform throughout its length.
In the above case, I think that the angle makes a difference due to the tapered plenum, thus the increased pressure at cylinder 4, 5 and 6. Try increasing the taper (relative to the plenum's baseplate) to add a bit more volume to the aforementioned cylinders, decrease the taper near cylinder 1 and lengthen the plenum's mouth to see what happens.