REassembled the main structure of the pylon tonight to include hooking up the flap connection and the engine mount tonight. Feels like lots of progress, though I just took it apart a week or two ago. The only problem encountered was the middle support (swept aft) is contacting the turtle deck on the right side despite both sides being shaved evenly along the hump in the turtle deck. I suspect because I trimmed a bit off the left side of the turtle deck everything got dragged slightly that way. It shouldn't be too difficult to fix and there is nothing structural about the issue, just asthetic.
