1994 Chevy Truck Exhaust manifold Install

I have a 1994 Chevy 1500 ext cab short bed 4wd 5.7 engine 4l60e tranny and 250K miles. Recently I had to pull the tranny to have it rebuilt and this required me to pull exhaust when I did this it broke the bolst of in the exhaust manifolds so I pulled them off the heads and had them drilled and tapped (i marked the manifolds to ensure that they were not mixed up at shop) but when I went to reinstall the exhaust manifolds I cannot get the bolt holes to line up == I can get the front four bolts in then the back two do not line up so I switched the directions and can get the rear four in and then the front two do not line up I am having this problem on both sides. Any help would be greatly apperecaited