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Reading all of this, I'm still not convinced you had all the wires hooked up properly to the plugs. I say this because I have personally made this error myself even though I have checked the rotation of the distributor to be sure, and then checked the cylinders, etc., and still got one wrong. And of course, motors will run this way but won't run all that well. Don't assume you know which way the distributor is turning, verify it with the diagrams and actual rotation.
One day I was invited aboard a 427 powered Commander and the guy was a very successful businessman in his particular field, but had no mechanical ability to speak of and admitted it frequently. We left the docks and things seemed just fine, but I kept smelling fuel. Finally I said, hey, let me take a look at that motor, just wondering if the choke had stuck shut, and when we opened the hatch lo-and-behold, there was a plug wire just dangling loose, lol, and when we hooked it up the fuel smell went away. I was quite suprised how well a 427 would run on 7 cylinders, the darn thing started just fine, we pulled away from the docks and took off, and it wasn't even readily apparant that one was running on 7 until I started to smell it.
Good luck on your project, you will find out what the issue is one way or another. Keep us posted.