I swapped the rods out for Crower H-beams with new Wiseco pistons and made sure they cleared, and went through and inspected everything in the head. Here's the pictures:
Engine Rebuild

We've run the lash all the way out (careful not to burn a valve up however), adjusted the lash countless times, checked the springs, retainers and lapped the valves, removed the Vtec followers, you name it. After six months of massaging the engine the best we can, my buddy and I are stuck without a clue. I've been hoping someone on the board has had this problem (knocking from the intake side, closest to the #1 cylinder) and knows what the deal is.