Any Ace hardware will have the HARDENED bolts. Make sure you use "Never-seize" when you re-install them. I'd guess someone has removed the A/C or some related brackets and replaced the same bolts using the castle-nuts as spacers.

While you have the manifold off either use a good straight-edge or take it to a machine shop and have the trueness checked. Use a tap and clean the threads. Be gentle, do not force the tap past the bottom of the threads as you can crack the head.