CEL -we'll have to wait for the code to be pulled.

Tranny leak -the mechanics either caused it, or missed it the first time they were under there. Either way, I'd hold their feet to the fire for it.

TOD lights -which ones are flashing? I was monkeying around with some sensors last week and found that by shorting the 4hi switch (not what you'd think it was for...) I would cause the AUTO light to start flashing. The front display lights would work normally. No red CHECK light as well.
If your AUTO light is flashing, it may be worth it to remove/clean/reinstall your 4hi switch (it's on the t-case).

PS pump and other seals -they are designed to keep fluids in, and don't do such a great job of keeping water out. It is possible that water forced its way past some seals and ended up in some places that it shouldn't be. Places like hubs, differentials, and even your power steering resevoir.