I had a similar issue. Van's indicated to me that I should expect this fitment to improve as the engine sags due to the engine mounts relaxing over time.
The area of interest is here (thanks to my friend and builder, Greg in Perth
for this diagram). This image is not necessarily to scale.
The following is described in more detail here on my blog
My bottom cowl sat too low relative to the intake. This is evident in the distorted profile of the CB-00032N Cowl Baffle Seal. It made placing the bottom cowl a challenging affair.
You can see the misalignment here. You're looking edge-on to the baffle seal: The bottom cowl is the lowest piece in the image, the baffle seal is folded forward, the next layer is the snorkel and the two pieces of (primed) metal are the CB-00033 Air Filter Frame Cover and CB-00020 Air Filter Frame.
One friend of mine adjusted the height of his snorkel. I took a different approach. The cowl was cut then reworked with a new buildup.
Without the CB-00032N Cowl Baffle Seal in place, you can see the better fitment.
Here's the final result.
It looks symmetrical and level relative to the right side.