Very nice write-up. I just installed a trick flow 1" on my 5.0 that is ready to go in my sport in 2 weeks. I elected to cut my coil bracket, and have a friend weld the mounting tab in a new location. Not necessary, but I figured why not since the motor is out. I also modified the throttle cable mount so it would still bolt to the coil bracket.
Did you encounter an issue with your trans dipstick tube hitting that aluminum EGR piece? I had to bend mine a little, but then again, I left everything bolted back there like stock. It looks like the PCM may get a little close so I may have to mount it at an angle like you did. Seems easy enough to do.
My spacer kit came with all the correct bolts. It was TFS-51520018 at summit racing. The only difference between the cobra and GT-40 kits are those 2 bolts.