I recently removed the IR cut filter from my camera and did not replace it with any type of clear glass. It has since lost sensitivity in the IR, which was the goal, but also focus ability in the optics. Can you explain why this is so?

What you are describing is a common issue people have when removing IR cut filters from cameras to do IR photography. Mainly, it is assumed that since the filter itself seems to have no optical power then removing it will have no effect on focus. This is not the case because even though the filter is has no optical power, it still changes the optical path length by refracting incident light. This in turn changes the point of focus. The problem can be easily corrected by simply replacing the filter with a clear piece of glass that is transmissive in the NIR such as BK7 or Fused Silica. It is important that this piece of glass be roughly the same thickness and index of refraction as the filter glass to simulate its optical effects without taking away from the IR performance of the camera.