You want a taper in your intake. Did you know TFS intake runners are tapered? Anyway, as the air rushes in, the taper causes the air to increase in velocity giving it more momentum. When the intake valve snaps shut, the volume of air moving into the intake and down the runner compresses at the bottom of the runner and then expands upward where it bounces off the air in the plenum and heads back down the runner. You have essentially have a column of air bouncing back and forth in the runner. The runners are tuned to a certain RPM so that the air bouncing back an forth will rush in just as the intake valve opens. This actually gives you more air in your cylinders than if you just had the piston sucking air directly through the intake port. This is why you get more torque with longer runners. Short runner intakes have less bounce and less air packing potential, but you are correct that they can give you more horse power at the top end. That's runner length, though. By not tapering enough at your initial point of intake, you're essentially lowering your low-end torque potential and your high end as well.
That's the gist of it. It may not be 100% right since I was explaining off the top of my head, but it's close enough that you should be able to get the theory behind it.
I don't really have more to add as far as your problem. Lower the fuel pressure and see if it makes a difference.
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351W 89 Mustang GT Convertible