A few solutions for you:
1. have the entire panel remade
2. cover and nicely trim a small piece of plywood and cover the hole. Then install the 6.5 into it.
3. take the panel off and trim a couple inches of wood away. Then stretch the vinyl into the hole and staple it to the backside of the panel. vinly wrap a small piece of plywood(maybe one of the other colors of your interior) to inset behind your side panel and mount the new speakers into it.
4. buy a 6x9 component speaker like MB Quart's RCE269