The issue here is that you moved the engine (by putting shims under the mount) to fit the cowl. This was your mistake. The cowl is supposed to be built to fit the engine. By this I mean that the engine needs to be properly mounted on the firewall. Planebuilder quotes the plans as mounting the engine at 0 degrees on both axis. So, this mean the engine mount should be flat on the firewall, and the engine mounted on the mount with the shaft inline with the centerline (thrust line) of the fuselage.

You have two choices. One, mount it the best you can and live with the cowl being "off center" with the engine. Two, cut of the cowl and rebuild it properly. My advice would be to cut the cowl off and rebuild it. By doing this you can take the time to verify that they engine is properly mounted on the fuselage.

Ken