Joker....Try to forget about the cartoon being the same as the films. I like the cartoon, but those are two completly different things all together..I see your pont but you can't compare.

As for Dooku...
I always thought he knew about the clone army. When he meets up with Sidious, they both mention the war and how the plan was working, or words to that effect, I take it Dooku knew all about the clones.

As for who orderd them, Lucas has said somehwere that the guy who ordered the clones WAQS seen in AOTC.
Who? Dunno
Why? Dunno

3 will sort that shit out.
As for the Obi- Wan thing..Dunno man, maybe he used the Force!