The only real issue for the intake manifold is not upsetting a rocker arm during install. I've never used guide pins, but that is the way to go if you have the space to do it. Last time I put it back together was the first time I unpinned and rotated the cams after assembly to check that the rockers were in the right place. I think its worth the time and peace of mind to know there is no binding.
Like flash said, do them one at a time and repin, you will keep the engine in time.
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2005 CRD "
Ol' Blue"
Red Ryder carbine-action, two hundred shot range model air rifle with a compass in the stock and this thing which tells time.
My build page- RL Komodo Rear and TJM Front Bumper, armored, lifted, JBA Steel D30, 4.10s and ARB air lockers.