2) What does Master Siphodias have to do with the clones and what was his role in the whole scheme of things? (Is he ever mentioned again in another part of the SW saga?) - I wish I knew. George Lucas really failed at that plot line. Big time.
3) I thought Padme was against building the army of the Republic? So why did Palpatine persuade Jar Jar to introduce the motion to give the Chancellor all the power in front of those other Senators? - He manipulated Jar Jar. Jar Jar thought he was acting in Naboo's best interest (even though he had been working closely with Padme for years. You think he would know better...)