You could use magnets rather than screws to keep the control cover on. Other people here have done that. No risk of splitting the dowels then.

Zooming in on the photo, the white lines on the end of the body look as if it's where you've sanded the wood smoother than the surrounding wood and the open engrain pores have filled up with fine sawdust. You'll probably find the lines go if you put some clear coat on. Or you could wet the wood with some turpentine or methylated spirit and see what is looks like wet, as that should tell you what it will look like with a clear coat on. It's also a good method to show up any scratch marks from sanding that are hard to see when the wood's dry.