How should I seal the joints? I was thing of drilling pilot holes and screwing the two together but what should I ise to seal it? Is there a good glue or slicone product? Or maybe some of the sticky foam sealing tape? Any ideas as to what would work best?

 

fiberglass them together.

 

Resin. Sand the bonding edges with rough sand paper and resin away.

 

I'm not sure if you've already glassed something up or not, but I try to make a frame out of MDF first, which I suspend in place as I 'glass away into my mold, that way the MDF frame is securely bonded to the fiberglass.

That way, I can be sure that I have a square and stury surface to screw my baffle panel to.

Honestly, I've never fiberglassed something without a frame 'glassed into it... but epoxy resin will allow you to securely bond already cured 'glasswork to the MDF you wish to secure (or a frame, that you can later screw the real MDF panel you want to attach, if directly bonding poses issues)