Thanks to a leaked piece of promotional art, it looks like we might have a strange clue as to the whereabouts of the missing Soul Stone.
The images show each of the Infinity Stones with the character they're most closely tied to: Captain America and the Space Stone (Tesseract), Star-Lord and the Power Stone (the Orb), Doctor Strange and the Time Stone (Eye Of Agamotto), Thor and the Reality Stone (Aether) and Vision and the Mind Stone.
Interestingly, the Soul Stone shows Iron Man, suggesting he's somehow the source of the Stone...
It's an interesting theory and it definitely fits the logic of the artwork. The problem here is that there's no real way to tell HOW the Soul Stone would be tied to Stark. There's some speculation that it could be linked to the element he created in Iron Man 2, but that would be an odd way to introduce an eons-old magical artefact.
Perhaps he'll just be the one to find the Stone in the forthcoming film?