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Exhaust manifold install. Help!!!

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Hello all,
I recently fubar'd my old exhaust manifold. Now I'm installing another one from my other motor that blew a couple months ago. Now the problem is that I have never installed one and cant find any clear how to's.
I got 4 bolts in but not tight. Top counting back. #2, 3, and 5. Are threaded but not tight. Then #2 and 3 have the bottoms in and not tight. Well now no other bolt holes seem to line up. It seams like they are cross threading. Once they feel like cross threading I stop and take them out.
I just need some pointers on how this can be accomplished. The truck is a 2006 mega cab 5.9l. Also the turbo is already bolted to the manifold. Thank you
 
I'm thinking studs are the way to go, if you have the means to pick some up. But you should try all the bolts first, chase any threads, I usually think those bolts take a beating heat cycle wise and could snap pretty easy and would think about replacing them anyway.

https://www.genosgarage.com/product/studkit8905-a/exhaust-manifolds

Since I work alone most of the time I would have to pull the turbo to do that just to make my life easier, save a little weight, but if you have good access and its not in the way, dont see why you have to pull the turbo.

Hear about the manifold shrinking, as the above make them a little larger might help the cause.
 
I would buy a new manifold. If the bolt holes don’t line up the ports will also have a slight mismatch. I go so far as to port match before installing the manifold,every little bit helps.
 
The one piece manifolds warp. Chase the threads in the head and blow them out with air. Sometimes taking a couple old bolts and cutting the heads off to make guide pins helps a lot too. Wire wheel the threads on your bolts make sure they are clean and put a bit of anti-seize on the threads. Torque to 40 ft lbs.
 
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