To join the MDF sides and the fiberglass base, my choice would be Duraglas. The trick to ensure a solid bond between the MDF and Duraglas is to brush resin on the MDF before applying the Duraglas. You don't have to re-resin the base because Duraglas sticks fine to resin. You can see some pics of proof here...
Painting over joints in MDF
The gap between the MDF and base doesn't need to be perfect, but should be within 1/4" to 1/2". Here's a pic of a sub enclosure with the MDF sides attached with Duraglas.
Make sure to lay up your fiberglass base several inches larger than where you expect the sides of the console to contact the base. Another thing that I prefer to do is to apply heavy duty aluminum foil over the masking tape with 3M Super 77 spray glue. Use a bondo spreader to smooth the wrinkles in the foil. You can also wax over the foil. The foil keeps the masking tape from getting super sticky from the resin/heat. Use compressed air to help remove the foil from the base after everything is cured. If you haven't done too much fiberglass work, follow this mixing chart for the resin. This chart is for 75 degrees F, so if it's hotter, use a little less catalyst.
If the top of the console is going to be flat, just use MDF. There usually isn't any point in making flat parts with fiberglass unless the part needs to be waterproof or lighter than MDF. Cut the side pieces and the top, dry fit them (screw together without glue) to make sure everything fits. Use CA glue or a little bit of Duraglas/Bondo (like tack welds) to first attach the sides to the base, so things don't move around when you are applying the full spread of Duraglas. Make sure to tape off any big gaps between the base and side with masking tape so the Duraglas doesn't just ooze out the other side.
How to attach the cupholder part to your console, depends on a lot of factors. It will probably involve stretching some material, resin, mat, Duraglas, and filler. Pictures will help. You should also think about what you plan on covering/finishing the console with before you start because that will determine where the "break lines" should be. Good luck!