Unless you drilled the holes for the cowl mounting screws very far back, you should be able to drill new holes 1/4" forward in the cowl, thus moving it back on the fuse, giving yo uthe clearance you need. You should be able to cover the top holes with a bit of covering, the bottom ones won't be too noticeable. Not to be crude, but if this is your first low wing airplane, you will be needing a new cowl at some point in the future anyway

The wheel pants can be beefed up a bit by epoxying a lite-ply plate inside the wheel pant where the nut clamps it against the gear. This stands up alot better according to my own "airframe integrity tests".

Have fun, its a great bird!