Engine Assembly Question

You have them right. The links are made to straddle those ribs. Looking at those latest pics, there's a mile of clearance! As long as the pushrods clear the holes in the heads, you should be good to go.
You’re not kidding, I had the holes enlarged when the heads were ported.

Looking at the pushrod checker vs rocker arm geometry I think I’m going to call B3 for a kit of some kind. I’ve never had to fix shaft rocker geometry