for starters depending on age, I'd replace the studs. If original, definatly replace.
as for the stud hitting the runner, pull it out & cut/grind it down the required amount until it clears.
as for bolting it on, as you are sliding it onto the studs, just as the studs poke through the holes, Start putting on the nuts (before the stud gets close to the runner. So sort of lean the top of the manifold back as its sitting on the top row of studs and just have the bottom ones coming through (thread or two)
once they are on, doesnt matter how close the stud gets to the runners (as long as it doesnt touch, der)