The alignment tool to check top plate alignment isn't terribly expensive. Next time you order something from Dillon add it on. I don't think that's your issue, but it's a good thing to have around. I run naked so not sure if the shell plate bearing kit could cause an issue there, but maybe?
If I rest my hand on the bullet tray while cycling the ram, I can catch the #3 pin with my index finger and pop it out and not really even feel it. Is it something that simple perhaps? The #1 pins are fairly small. I can't think of anything else, but I'm planning to load up some BR tonight and tomorrow and will really pay attention to that particular pin.