Well, if it was me, I'd try to isolate the noise. I'd put my car up on blocks, on all four corners, open up the hood, start it up, and investigate things. Have someone run it through the gears, while you roll around on a 'creeper'. Use a stethoscope, et cetera.
I now this sounds silly, but how else are you gonna find where the noise is coming from, you know?
