If I'm reading you correctly, the test pipes have been in since you've had the issue.
Lower gears, 2-3k rpm, directly under the car. Sounds exhaust related to me (primary cat delete). Have you checked the test pipe connections? Even if they're sound seems some vibration could emanate from them. I just installed Akra Evo this past weekend after running only an axle back -- noticing all kinds of interesting sounds, resonance, and perhaps some vibration after cat delete. Nothing quite as consistent as you report though.