Trevor, lets make sure we are talking about the right case. When you say you had water in "the rear end" i am assuming you mean the differential case behind the transmission?? if so, the water came from rain around the transmission lever. the transmission case, the differential behind it, and the PTO housing behind it are all connected internal. you fill them thru the transmission fill plug on the left side by your foot. it takes about 2 gallons and should be a good trans-hydraulic fluid, 20wt. you can get this at the farm store, or wal mart.
There are three plugs to drain the system, one under the transmission, one under the differential and one under the PTO. you are draining the same oil, at three levels. If you are talking about the final drives (the little tin pan) at the bottom of the drop box, setting inside the rear wheels, then yes you need 80 or 90 wt gear lube in them. you must remove the pans and clean out the old oil. after reassembly you add oil thru the 1/2 inch pipe plug. i havnt seen a final drive with water in it too often. last of all, yes you can do exactly the same thing with the CA.

I believe the B, C & CA have only two drain plugs; one under the tranny and one under the PTO hsng., unlike the WDs & WD-45s which have 3 plugs (5, if you drain the hydraulic system). The Bs & Cs hold 7 Qts with the PTO option, and the CA holds 8-3/4 Qts.