For what its worth, I've done some pretty extensive dyno testing on a few different intakes, including the factory Cobra Jet and the Blue Thunder intake, to compare the low riser and medium riser port configurations on different cylinder heads. At least up to 500 horsepower, the port configuration doesn't matter. What this means is that you can put the Blue Thunder intake with the low riser ports on the medium riser style heads, or use the Blue Thunder intake with the medium riser ports, and you will not see any significant difference in performance. Similarly, you can use either port version of the Blue Thunder intake on a factory low riser set of heads, and you will also not see any significant difference in performance. The engine just doesn't care too much about this.
Here's an example, from data in the appendix of my book. On my 390 stroker engine, which used Edelbrock heads with the normal medium riser port configuration, dyno results with the two different versions of the Blue Thunder intake were as follows:
Blue Thunder intake with medium riser ports:
Peak torque 504.6
Peak HP 497.0
Average torque 479.5
Average HP 409.3
Blue Thunder intake with low riser (Cobra Jet) ports:
Peak torque 508.7
Peak HP 497.1
Average torque 482.0
Average HP 411.5
In this case, the manifold/head combination with the mismatch at the port made more torque and horsepower! Of course, it is also worth noting that accuracy of the dyno is probably around one percent, which means that these two sets of measurements are within the measurement error range of the dyno equipment. So, there is effectively no difference between the two intake manifolds in torque and horsepower production.
This is counter to long standing beliefs that many people have about the need to port match, but I have quite a bit more data to back up this statement. The port mismatch between low riser and medium riser version is at the floor of the port, and it just doesn't make much of a difference on these engines.
I haven't run tests like this on higher horsepower engines, but there I would expect the differences to be a little more pronounced. However, for most FE engines, there just isn't much to be gained by matching a medium riser intake to a low riser port, or vice versa.
