Manifold warped, bolt holes don't align? Ultra-common problem.now I have a new headache.
stock exhaust manifold doesn't bolt up to the head on the driver's side.
Ideally, you'd cram the manifold-spreader tools into the manifold before you pull the bolts out. The manifold never has a chance to distort when removed.
Things are trickier when the manifold has already distorted. Sometimes the manifold spreader tools can "jack" them back into position, sometimes the manifolds crack in the process.
MAYBE you're better-off to buy a new replacement manifold or two. The quality is pretty low, but it can be better than fighting with an original that tweaked. The new manifold may need to be planed by a machine shop before you install it--they can be pretty bad out-of-the-box.
Good time to be thinking about shorty headers.
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