Does an increase in temperature cause an increase in the FIR waves, or is it a deeper penetration to the body? If I run low temp, will I have the same effect as at higher temp?

Of course the temperature increase will cause an increase in FIR waves. The more energy, more radiant rays, the more penetration. Just be careful not to get low temperature burns, it is quite possible even using a warm mat.  

If you run it at low temperature for longer time it is a safer, more cumulative treatment.