[ame="http://orbithangar.com/searchid.php?ID=3737"]International Space Station v.3.2[/ame]
This is ISS 3.2 aka Thorton's ISS.
I recommend opening the various scenarios and take a look at what it does with both the LC-39, and as well as the Shuttle Fleet orbiter. You will also notice that you can add in runway search lights too if you want.
I recommend attaching the bay vessel like those scenarios do, use the Shuttle Fleet's own integrated attachment system to put your own payloads in, use Launch MFD to find your launch window, save the scenario at half meco time + 540 seconds, that way you will have time for the countdown and automatic launch sequence, and launch in plane.
Erase the TIMER lines you will see for both the LC-39 pad and the shuttle's bay vessel, enter your desired launch heading as laid out in the Shuttle Fleet manual. The Pad will be animated, the Shuttle will launch automatically, no need to press ITEM 777 into GPC MFD or anything like that, sit back and watch the show.
I might be skipping some steps by accident, this is just a thing I have done so many times, i have set up I dont even know how many custom Shuttle missions for my VSA using ISS 3.2's add-ons like this that I just kinda go into robotic mode.