Are we talking about factory headers or aftermarket?
Well anyway the FE's are the worst motors when it comes to installing exhaust manifold bolts in, especially when it comes to the CJ bolt pattern with 4 bolts per port (32 in all). This is one of (if not the main) reasons I'm going to notch my towers for the extra 3 1/4"-3 1/2".
As already mentioned I'd use PB blaster on it for a few days & take it slowly. As for a exhaust leak if I remember your main thread on this car it alreay has a bolt missing from that side so the chance for a exhaust leak is high.
1968 GT/CS clone restromod in progress of restoration being reborn with a 390FE, 4.11 limited-slip Ford 9", 17x8's Bullet edition silver matallic rims, Raven Black paint, Deluxe black interior, & to many other mods to list.