First off, I've gotten octalink cranks from Shimano that have not come with self extracting dust caps. In fact, I got some new ones for a project two weeks ago. Second, something was cross threaded if you stripped those threads all the way down. It's easy to do, but you should bear that in mind in the future. The Octalink/Isis cranks do need a different puller head but you can get around that. Depending on how the cranks are set up there's a common US coin (nickel?) that works with some of them. Alternatively you can use a properly sized washer, or get a short wooden dowel rod, slip it inside the spindle, and cut it to length. To do remove the second arm, remove its bolt, then put the bolt back into the first side of the spindle and repeat. Depending on how your crank spider is made, a standard three arm puller often works as does a small arbor press, although those last two may permanently bend some of the arms on your spider depending on how it's set up. Bike shops (or your successful boiling water method) are also good alternatives. I do NOT recommend drilling a hole in your crank. People have also been known to use torches, although I don't imagine this will do good things for your crank if you aren't careful.