It's plugged there isn't anything you can put there with the throttle linkage. I originally planned to have the breather tube there until I realized it wasn't going to work.The build looks great man! When I got mine back on the road in a more appropriate street trim I have more fun than I did as a "race car."
Thanks for posting those last two pictures. I've been trying to figure out if those valve covers will fit under a TFS track heat intake. I really don't know the height difference between mine and a cobra manifold but I have a 3/8" and worst case a 1" spacer I plan on trying out.
Did you plug the passenger side rear hole?