If the air filter is in place the lower cowl can not be placed as there is contact between the two. This is significant. I read that this is also not uncommon.
I took the advice of another builder and machined out a tiny relief hole for the head of one of the control cable retaining screws. This allows the airfilter to move upward significantly. This was all that I needed.
However, I have also ordered and will use a K&N reusable airfilter (E3120) which is a tiny bit shorter; this will give me a good margin. The K&N filter is a common addition as it allows more airflow than than the AeroConversions product and it is resuable.
Also corrected the heat shield I had fabricated for the exhaust as it passes over my fuel line. I added a half-inch standoff which should allow it to actually do it's job.