That rod fitment issue is a real downer. I feel your disappointment. Any chance the rod bolts are just wrong? Seems like a big oversight on the manufacturer's part. When I go to Jegs, the nut style is hex but your's looks to have 12 point + thick washers.
That rod bolt looks like it's protruding well into the pickup tube. I don't think any clearance will fix that, at least from the picture.
Edit: Wow, my bad. I see you're talking about mains not rod bolts. Shouldn't post before I have my morning cup o joe.