Mounting exhaust manifold to Aerovee with exhaust flange gaskets. Drilled flange keyholes to round the straight section of 'keyhole' to provide thread clearance for square bolt alignment.
Much pulling and pushing of exhaust tubes to align and install bolts. Technique for final flange (#1 cylinder in this case) was to pull flange into position with opposite flange bolt in place. Pull the exhaust pipe while tightening opposite flange bolt. Last flange bolt could then be aligned and tightened.
Flange bolt bottomed before bolt head engaged flange facing on cylinder #1. Used washer for thread take up. May try running a tap into the hole.