Shorter runners should reduce a little of the peak torque in favor for broader torque curve. The supercharger will more than make up that little bit of loss, while adding to overall power output.
One thing that stands out is the two oversize throttle bodies are feeding a nicely sized plenum, yet the engine is till breathing through the most restrictive portion of all the L-6's, the stock EFI runners! opening up the ID of the runners, full length to at least match that of the cylinder head, will be where your biggest gains come from. Even if the runners were appropriately sized, one of those TB's feeding the plenum at whatever location is deemed appropriate should not impede power production vs. using both, and is more than adequate to deliver plenty of air even to a hot L-28, N/A or boosted, especially with stock EFI runners. The runners of the stock EFI manifold are only 53% the area of the intake valve itself which in my opinion for building a custom or modified EFI intake, is the first place I'd spend any time trying to adjust, then move on appropriate plenum sizing.
Sort of a tangent, one could use the SU carb manifolds which are shorter in length yet have larger diameter runners than the stock EFI manifold. 2 routes to go with the plenum here. Either bolt the plenum directly on the manifold with a nice air horn for the entry and then mount a TB any where on that plenum, or, bolt a couple of 2" TB's, (2" would be overkill, but only by a little), on those manifolds like member z-ya did here http://forums.hybridz.org/showthread.php?t=124201, and whatever size plenum one desires attached to the TBs, small air horns on the TB's inside the plenum. That would give you the shorter runners that are more closely sized to the engine, TB's aimed nicely at the runners entry, and leaves a plenum that is always at atmospheric pressure ready to serve the engine.
My apologies if I went too far off topic. If so, let me know and I can delete it.