The mystery is difficult to completely work around, but in the work I've done so far I think it is more logical. Obi Wan and the Jedi are not trying to figure out who created the army in the first place, instead they are surprised to find that a bounty hunter has been used as the template without their knowledge. It is more of a suspicion that perhaps something fishy might be going on on kamino. And their suspicions are confirmed when jango is behind the attack on Padme. It still sounds a little convoluted but given the source material I think it's the best decision (It satisfies me, at least). An added bonus is the rivalry that develops between obi wan and jango after obi wan recognizes him on coruscant and follows him back to kamino.

I hope to have a very rough workprint finished either this weekend or in a month (I'll be going out of town for a while starting next week). I'd love to have someone watch the full thing and give me feedback.