I recently installed an edelbrock performer intake and have slowly been cleaning and reinstalling all the parts.

I found that due to the performer intake being higher than the stock intake my ignition coil no longer fits. The coul bracket doesn't lift it high enough.

Also has anyone previously installed this intake on a 66 Ninety Eight 425? With the new intake and factory air cleaner installed it almost looks like the air cleaner will hit the hood. I can close the hood but it looks so close I am worried about it hitting when the engine moves.

 

I take it that the rocker swap was successful.
Take a 5' long piece of 1x2 wood across the fenders to see if the air cleaner will interfere with the hood. You can gain 1/4" clearance by swapping out a thick carb gasket for a paper thin one. Use a custom length air cleaner hold down bolt, too. Otherwise you may have to mill the carburetor pad on the manifold, or use a different air cleaner. I ran a Torker on a 455 equipped 66 Cutlass, with a q-jet, and had to use a Moroso 3" air cleaner to clear, and it still rubbed. I can not imagine that you would have less room than that.
Any straight edge 5' long will be your friend.
Get a long bolt, and a spacer for the coil mount bracket.
Jim