2011 5.0L, intake manifold wet and strong fuel smell.

So recently I removed my intake manifold off of my 2011 5.0L. Before I could even get the throttle body off it had a strong fuel smell. After removing throttle body the entire inside was saturated in fuel. I then began removing the fuel rail with the injectors. The injectors were relatively new along with O-rings and I keep my motor very clean internally. I pulled the plenum off and gave it a cleaning, replaced the individual ports gaskets, then upon re-installation I noticed something odd.
All 6 bolt holes lined up without any trouble, but I noticed that the ports for the injectors no longer had a clear shot straight down to the valvetrain. Then I noticed after tightening down the manifold that it just wasn’t pressing/ seating down like it always does. Please has anyone experienced this?!?
 
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