I believe it is coming from the input side, because it does not change with the range selection and seems tied to engine rpm.
Does it make the noise if you push in the clutch ? It could be clutch related.
Without moving the tractor, increase the rpm's to to max, does the noise still increase with the rpm's, I am guessing they will.
Drain the trans oil into a clean container and see if it is clean or has metallic particles in it ( looks gray or silver) Either would be bad. You could even run a magnet through the old oil and see if it picks up any thing. Unless the oil is clean, replace it. Replace the trans and hyd filters, then see if there is anything in the old filters.