The Sifo-Dyas issue is the EU writers having to clean up what George messed up. IIRC, the character was originally named Sido-Dyas, and would have been Darth Sidious posing as a Jedi Council Member to order the army. But this might have too obvious to the Jedi or the audience, so George made some changes and Sido was changed to Sifo. Jango was then introduced into the mix as being recruited by Tyrannus on the moons of Bogden to account for the creation of the clones and to legitimize the newly created character of Sifo-Dyas, who was now a legitimate Jedi who still might have ordered the clones and [insert murky plot here].

This created the biggest plot-hole of episodes 2 &3. By the middle of AOTC, Obi-wan Kenobi knew that Jango Fett was affilliated with both the cloners of Kamino as well as the makers of the droid armies of Geonosis. And that doesn't sound suspicious to anyone?