I would agree that the plenum volume appears minimal. Keep in mind that the purpose of the plenum is to simulate individual intake stacks. In other words, the flow velocity, within the plenum, should be quite low. As I understand your modification, you have not changed the plenum cross sectional area perpendicular to the runner axes, so I'm not certain you have significantly changed flow velocities at the runner inlets.
Manufacturers minimize plenum volume to minimize part cost and provide more engine compartment room. So, like everything else, it becomes a compromise.
Longer runners also cost money, so, again, the desires of the engine developers might be compromised. Those looking at the dyno output want short runners to yield maximum power. Those calculating performance want longer runners to maximize acceleration performance. The bean counters don't want any runners at all, if it'll save a buck.
You say you want to tune for about 6000 rpm. I assume this is approximately in the middle of the rpm range you encounter as you go through the gears. This means the distance, from intake valve head to plenum, should be about 13 inches for maximum effect. The next "harmonic," or whatever you want to call it, hits at a length just under 10 inches, but it is not nearly as strong.