Activate the SCENARIO EDITOR in the Orbiter launch pad.
Open a launch scenario.
Press F4.
Scroll down to the tab labeled CUSTOM.
Highlight SCENARIO EDITOR.
Once the editor opens, you should see the Spacecraft and an item called LAUNCH TOWER. Highlight it.
Click the button to the right marked EDIT.
At the next screen, click LOCATION on the ON THE GROUND tab (to the right).
Adjust your camera position so you have an external, aerial view of LC39 and the Saturn V.
By using the Longitude, latitude & heading buttons, you will move the pad left, right, forward and back as well as the rotation of the pad. Play around with these until the pad is in the correct position.
Once you are satisfied with your work, go back to the front page, highlight the name of your spacecraft and move it onto the pad. Same proceedure EXCEPT when you get to the page with the lon, lat & heading buttons, look at the box on the lower right marked COPY STATE FROM. Click on the name of the pad and your Saturn V will move into position. If you need to fine tune it, use the lon, lat & heading buttons.
Really not as hard as it sounds, Just takes a few minutes...