I believe I've fixed all the major issues with using the Mouse Emulator mode in games. In hindsight I listed the mode on my website a few weeks too early and this is the first version that is truly playable.
It uses Track IR for both head rotation and movement. Track IR isn't ideal because it wasn't designed for the distances I am using it at. I may write my own system, however it would incur a significant performance cost while Track IR takes very little performance relatively speaking.
Voice Attack is used for all commands other than looking and moving. Voice attack also isn't ideal, as it can fail commands. But it's the best that is available. I haven't found a way to put buttons on my gun that also do not disrupt the shooting experience. Will keep thinking about solutions.