If I'm not mistaken, there are two PTO control levers on that tractor. One acts like a master - that is, PTO engage/disengage. The other is the PTO speed select, which has sort of a quasi-neutral position between speeds. Try disengaging the PTO to see if the noise persists. Try first with the speed select in the middle position, then with the master lever in the Disengage position.
Did you verify your gear oil level? I should have mentioned also, that some owners have had a problem where not enough gear oil from the transmission flows forward into the mid-connect box (creeper or shuttle, whichever you have). But you probably have to remove the mid-connect box cover plate to check that level.
//greg//