Um, I feel embarrassed about even responding now. Just checked out your photostream on Flickr. I'm simply not worthy... <hangs head in shame>
Ha, that's hilarious. I'm a long-time technical guy (computers), but haven't had time to really dig into the technical details of photography, and I'm pretty much still winging it. I'm hoping to have more free time this year and change that, though.
You mention having difficulty with manual or auto-focus so I assume it's not an issue with not finding a good high-contrast point for the autofocus to work with.
I'm usually using this lens for video, and I always manually focus video since the continuous focus on most DSLRs is slow. I've got a SmallHD external monitor with focus assist that helps, too. But even when using auto-focus and getting the "green box" focus confirmation, the video will still be out of focus. So I'm thinking you're right about moving the dome out. I've never had this problem with other cameras/lenses/ports, but this is the only lens where I'm not following the manufacturer's recommendation.