Manifold attachment/alignment

I can only speak of Evo and Twin cam as I haven't futzed with a shovel, however, raise the tank and remove the horn get all the room you can.

You should have markings on the manifold flanges one front one rear,

I slip the flanges on the manifold and then the rubber o-rings, narrow side toward the intake, they will allow some movement but the o-rings should be tight.

Then I put the lower rear bolts in place and slide the manifold and flanges over them, and thread the front bolts, then work around the manifold to tighten them down, some front then rear. Keep the manifold level.

Thats about it sorry hopefully CD will jump in.