I'm looking at the Spec S-works road shoes right now. I have a couple questions.
1. Are you sure the shoes are not a tad large for you? This sounds like a "foot pumping in the shoe" issue. They need to fit more snugly than a lot of people think.
2. I'm looking at the tongue of the shoe. It comes a long ways back in the shoe. Can you confirm its the side of the shoe versus the side of the tongue that's causing you pain?
If it's the tongue, maybe you can just trim it back a bit.