I'm doing the swap right now and have the same issue with the larger intake ports on the 2.5 Fusion engine.
Here's what I'm doing that I think might work. I believe that if I can nudge the manifold up just a fraction of an inch, it will seal.
I smeared used motor oil on the rubber intake gaskets and then test fitted the manifold to the head. You can see how the gasket isn't making good contact with the head above the port. Easy to see why there are leaks. The gasket imprint on the bottom (below the port in the head and near the bottom of the picture) is well below the bottom of the port in the head so we have quite a bit of space to work with there.
This is another shot after a couple of modifications that will be described below. There's not much room to spare but the gasket is now making good contact on the head.
There are two small round plastic dowels or nubs on the lower part of the intake manifold, right under the ports. They go into holes right under the intake ports on the head and it looks like they are there to help align the manifold when installing it. What they also do though is keep the manifold from moving up slightly, so I used a hacksaw blade and a file to shave off the top half of the dowel (center of picture). It's possible that they could have been entirely cut off with the same effect.
Then I bought new intake bolts, but fully threaded bolts instead of the stock shanked ones. The shank is just a little larger diameter than the threaded part of the stock bolts but a little can be a lot when we're trying to move the manifold just a smidgen. The short bolts (there are 6 of them I believe) are 40mm long and the longer ones that go on the right side are 80mm. I had to order the longer ones online as I couldn't find them locally.
Because the round metal inserts in the intake (through which the bolts go) are larger diameter than the diameter of the bolts, the intake can slide up just a little once you shave down the plastic dowels and get rid of the shanked bolts. In these shots you can see the bolt head in the upper and lower positions of its range of movement within the metal insert in the manifold.
I can't say for sure that this will work but am hoping so - I just got the engine set back in the car and still have to hook everything up so it will be a few days before I have time to get it running. The custom fabricated plate may be the best way to go but I didn't want to go to that much trouble unless I have to, and also want to maintain a fairly stock appearance.
I'll let you know how it goes.