Definately take the MSF course. We spent the first hour getting used to the "friction zone" on the provided bikes, so you'll pick up the clutch process pretty well. You'd do as many "engage / disengage" cycles as you'd do in a month of normal riding. You'll also get used to shifting as there's a lot of exercises where you're going back and forth between 1st and 2nd gear.
To be honest, my biggest "fear" going into the class was being able to coordinate the shifting process, as I just couldn't picture it in my head (having driven a stick-shift car for 20 years). Once I was in the class, I was so excited to be there that I forgot that I was nervous about learning how to shift a bike, and before I knew it, I had already been doing it. That night I had no problem practicing in my head how to coordinate the hands and feet.
So while the "theory" of driving a manual is helpful, just in understanding when and why the bike will start to move forward, I don't think it's necessary. IIRC, at least 2 people in my MSF course said they had never driven a stick shift. (One of which was a 60+ year old woman who ended up kicking everyone's ass in the "figure-8 box")
If it helps, I walked into the MSF class having never sat on a motorcycle before, and came out feeling like I had a pretty good idea of what I was doing. I bought a bike 2 weeks later and have been loving it ever since.