Mouse Acceleration/Stutter due to frame-limiting

[PastPerspective]

Hey guys, I bought Deus Ex: Human Revolution on Steam, to find that it runs at such a high frame-rate that it causes my PC to overheat. I tried limiting the frames to 60fps using DXTory, as I do in Dead Island; but it's giving me slight stutters and mouse lag. I've also tried enabling V-Sync but I get extreme mouse acceleration. I was just wondering if there were any alternatives to DXTory, or perhaps another way to keep my PC temperature down? I tried using MSI Afterburner to cap my frames to 60, but this one also causes the game to stutter and lag. Thanks in advance.