Today I transfered the basic character model and rig into the game prototype. It was a little chalenging but I managed to ajust all the scales and line the camera and empty shooter up relatively well.
Next I added the logic bricks to the character that the previous cube had as well as all the properties.
I also spent a lot of time figuring out how to stop the glitches with the running. There was previously a problem where the character would glitch if more than one movement key was pressed at once. I stopped this by specifying that they were on different layers and making them blend slightly.