I have a Poenix extra, but unfortunately I have not built it yet. I few pic would help if you have a camera. I assume you have moved the engine out as far as it will go on the mount and you are still not out the 4 3/4 " you need. This length is only so that the cowling will fit. Try putting the cowling on and move the cowling toward the canopy to see if you can get it close enough. If that doesn't work you can add 1/4" spacer on the firewall, drill through it into your firewall and put new T nuts through both. As for why the pitts muffler does not work, I am at a bit of a loss. Are you saying that the muffler comes into contact with mount? Are you mounting your engine with the head down or sideways. The pitts mufflers are made for one or the other. Is your mount upside down as well?

As for the throttle tube. Just drill another hole and move it to a location that will line up with the throttle arm. Plug old hole.