The Multi-power valve in the clutch housing either energizes the clutch pack, or dumps oil back into the transmission. The regulator valve will only "shuttle" slightly within the housing to regulate line pressure. I don't believe that either could stir the oil in the fashion that you mention.
More likely to be a split in the internal feed pipe to the input housing and M.power valve, BUT the multi-power would be rendered in-operative, I believe. Is the multi-power working correctly?
If you are sure that this noise is coming from the transmission, I'd still bet on a failed bearing on the PTO drive side. It's possible that if one or both of the pump dowels have broken, it could also give you a similar noise. This would be coming from further back under the seat area.
The relief valve is set back in the centre or diff housing, on the auxillary pump. Not much chance it could stir the oil in the transmission to that extent.
The filter you described is the linkage hydraulic filter. There is most likely a second filter for the auxillary pump, depending on the configuration and serial number of your tractor. Apologies, I posted a pic of the standard transmission instead of the multi-power box, Evan.