For the cylinders, you can try using a flexible bellows that covers the entire rod, so that it can still extend and retract while sealing out dirt. Here's an example of the bellows used on a water jet cutter to prevent backsplash from hitting the parts that move the cutting head: [link]
Hmm, you make it seem like a fairly basic process! Did making the lineart by hand (versus the computer) speed things up a bit? Thanks man!