I've removed all of the brake shoes, as well as traction tires. Looking at the rods closely from side at top of engine with shell off - nothing is touching or rubbing. Crossheads are not rubbing anything and they're not hitting the frame of the engine or anything. Agh, doesn't make any sense. Could it actually be a problem with one of the wheels?
Also to note: I hear the noise mainly if the engine is moving forward. I barely hear it when going in reverse.