Staking the nut refers to bending part of the nut onto the flat spot on the shaft. You will see a little indentation on the shaft, and you will get a screwdriver or something and flatten part of the nut onto the indentation. This keeps the nut from coming loose. I would probably go back and do it for good measure.

Gear oil should NOT be black. Different brands are different colors, but the cheap stuff I use is simmilar in color to new motor oil. But healthy gear oil should NEVER turn black like motor oil does. Some leakage is expected when you take off the flange to change the seal. If your t-case is filled properly, you should see quite a bit pour out. Did you refill your t-case after changing it? It could have been low on fluid to begin with, or have some bad oil in it. It might be a good idea to drain and fill with new gear oil.

I've heard of using RTV on the seal but never actually done it. I don't have leaks either.