Here's what I usually do.

1)Standard sized TV/movie cels get a new bag. All 
layers are also bagged separately. Small to 
medium pan cels usually stay in the same bag 
since I don't have any bags to fit them. If the 
bag is in bad shape I tape a few new smaller bags 
together to fit. Large cels (too big to fit in 
largest Itoya) get professionally framed (I don't 
trust my own framing skills)

2)I remove all staples and tape very carefully.

3)Depends. If the layers are not stuck I gently 
clean with either water or small amount of 
rubbing alcohol(to be quickly washed off 
afterwards). If the layers are stuck, I don't try 
to force them apart nor try to clean them since 
I'm worried about damaging them and getting 
cleaning agents trapped between layers.

4)I scan out of the bag. The only exceptions have 
been a few cels that came to me already framed. I 
just scanned them through the glass and hoped for 
the best.

5)I keep the sketches separate from the cels 
since they take up too much room in the 
portfolios. All sketches from the same cel 
(anywhere from 1 to 30) share the same bag. I 
keep the backgrounds with the cels. Since the 
portfolios are supposed to be acid-free and the 
backgrounds shouldn't stick to anything, they are 
not bagged separately like the cel layers.

6)Like everyone else so far, I really hate stuck 
sketches. If they are only lightly stuck I just 
work at them very slowly until they come apart. I 
have been tempted by the freezer method, but 
haven't tried it yet. I had a few that were VERY 
stuck and paid a restoration company to separate 
them. I have mixed feelings about the results and 
feel its probably not worth the cost unless the 
cel is very valuable.