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i am in the middle of doing my headgasket and i sent the head out to get milled, I Pulled the cam out before sending it so they would not nick my valves.

Anyway, The question is since i removed the cam, will the head's TDC marks no longer line up properly or can they be out 180 degree's?

I Did not remove the cam gear from the cam.

 
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Your timing marks will still be in the correct location. Just make sure you put the head at TDC and the block before you put them back together.

Then they will match up perfect.