deffinately, without a doubt, rebuild the pto shaft assy or repalce it. that thrust play will get wirse and cause other harder to repair problems if left unatended.
I like to flush wet sumps with kerosene or diesel or mineral spirts, mixed with some atf type f or dex/mer 3, plus some 90% rubbing alcohol. 1-2g diesel to a quart of atf to a pint or 2 of alcohol, depending on how bad the water was. victory lap around the yard and drain.