Intake Alignment Issues

I bought a new in the box Edelbrock 4bbl manifold to convert my RB over to MPFI. The manifold was significantly too wide. It wasn't really possible to see where the manifold ports were lining up on the head ports by looking down the intake flange.

I applied some grease to the head flange along with 4 small spots of Permatex to keep the intake gaskets in place and the gasket perfectly lined up with the intake ports. My heads are ported and the gaskets now stayed fixed to the heads in the correct alignment to the ports.

I smeared a thin film of Permatex onto the manifold flanges and torqued the intake onto the motor. I left it sit overnight.

The next day, I pulled the intake, and the gaskets remained stuck to the intake in the exact position of my head ports. This revealed that the manifold was sitting up too high on the heads. The bolt holes were perfectly centered at this point, but the manifold needed to have both faces cut to lower the manifold towards the China Rail.

My local machine shop was very familiar with this process, and stated that it's typically the head side that is cut so that the manifold won't fit only this motor. That is a non-issue in my case, so they cut my manifold in 2 steps. I refitted the intake using the same technique described above so as not to overcut the flanges.

They ended up having to cut .100" off both sides of the intake to center the ports properly. As a result of this, I had to use my die grinder and a small carbide burr bit to elongate all the intake holes, so the bolts would not hold the intake up too high or not line up as you are experiencing.

It only took a few minutes to carefully elongate the bolt holes for clearance and several checks to ensure I didn't need additional clearancing.

I then refit the intake back onto the motor with another intake gasket set in the same manner as mentioned above, pulled the intake and shipped it off to Wilson Manifolds for an Intermediate porting job. As fas as I know, that is the only way there is to accurately indicate the exact position of the head's ports onto an unported intake.

Once the intake comes back, I am confident that the port and bolt hole alignment will be as close as possible to optimal alignment on this specific engine. If I can remember, I'll update this post with the results.