I had a similar problem by sinking my 250sx in a puddle. I did an engine flush with diesel and then again with ATF and 10w30 , ran it a bit, then changed to 10w40.
I also changed my rear differ oil ( SAE 80 ) and it was a light chocolate milk color. after I drained it I squirted a bunch of gear oil in there and pushed the machine up and down the drive way, let the new oil mix with the residual, drained it....did this about 3 times and then it was all coming out the nice clear clear yellow color.
1985 250sx (Lemon)
1985 250sx (Ruby)
1985 250sx (Garnet)
1985 200m (Hunter)