Don't screw with the taper bores-they're there for a GOOD reason. Notice when installing the upper IM that there is play where the bolts pass through the upper and bolt to the lower. Notice also that it's basically impossible to know if the bores (upper to lower) are aligned. The mismatch means that airflow will not hit the "lip" and become turbulent. This applies at the lower IM to head interface also.
Another reason to leave the taper alone is that it causes the airflow to speed up as it is squeezed into the smaller bore area (Bernoulli's Law, IIRC).
