There are many products out to bond various body components together. Your local auto-body supply store should have everything you need.
There are SMC compatible fillers and panel bonding / fillers. Evercoat makes a product called Vette Panel Adhesive that is SMC and FRP compatible. It is what I would use to bond panels.
3M also has an automix system that is urethane based for bonding and filling various panel types together, to include the PRIM, RIM, SMC, FRP, etc...
Since you have decided to create your own, The SMC portion needs to be ground down lightly with a very course sand paper / grinder before you use any FRP. The glass Mat will work, but I would recommend an SMC compatible resin. To work with the RIM/PRIM, I would go with an automix...
Examples:


-Dave