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One method is to put your manifold in place between the spigots and then start tightening the head bolts. Look at the gaps between the head spigots and the manifold to see if it's aligned correctly. Adjust the heads as needed.
Another method is to install the manifold without the o-rings. Install the clamps and tighten them, and the loose heads will align themselves to the manifold. Now tighten the head bolts in the standard crisscross pattern to 15 or 20 ft. lbs. Remove the manifold and finish tightening the head bolts to the proper torque specs.
You can make a leak tester to check your work by fabbing some type of cover for the front of the manifold. A piece of metal with holes drilled to match the holes of your manifold, and another hole for some method to connect an air line, works fine. To test your manifold-to-head connections pump about 5 psi into your contraption. Yeah, you gotta make sure both your intake valves are closed! Use some leak detector or make some with soapy water. Slosh it on the head-to-manifold joints and watch for bubbles.
When you are installing those dang o-rings, roll 'em up onto the head spigots, but make sure they don't twist when you slide them into the gap. Then before you put the clamps on, take a wrap or two with some electrical tape around the o-ring. Use some good tape, not the el-cheapo crap from the bargain bin. I like either Scotch 33 or Scotch 88. 33 is thinner and more flexible.
Some folks don't like the tape routine. It does goo things up as the tape gets warm. And that is one reason it helps seal things. The next time you pull the manifold off, it easily cleans up with some good ol' gasoline.
You folks with later model Shovels don't have to mess with the o-rings; you've got those nice wide sissy bands. But things will still last longer if you align the heads and intake manifold.