Skerry centerboard trunk has gaps with frame

I am building a Skerry, and I'm about to install the centerboard trunk. Notches in the trunk are supposed to fit into notches on the frame. Things didn't quite line up, so I sanded the trunk. Too much (see pictures below). My thought was to create some shims and epoxy them into place. Can anyone recommend better options?

 

  That's what I'd do.  Make the shims an easy slide in.  Don't make them wedge in the gap.  Slather liberally with thickened epoxy before inserting.  Clamp/screw. Clean up and hide any remaining gaps w/ fillet mix.  My skerry trunk also wasn't a perfect fit, although it was close enough. 

Mummichog, thank you for those details.