I haven't checked the dowels, I wasn't aware of that before. But, all of the rockers and cam lobes line up really well, so I wouldn't think it would be a major problem like that. I'll check that this weekend though to make sure.

Here is the worn out #4 intake stud (after ~2500 miles):


It's not an hourglass shape. It's actually worn quite flat, you can feel it pretty easily. Plus, you can see there is some pitting. It only really started making a lot of noise over the last 200 miles or so, so it's not like it was really loose for 2500 miles. It was pretty tight and quiet until recently. ANy ideas what could cause this?