I'm in the process of doing the stereo on my Vert... The idea of porting the trunk sounds ok... it shouldn't be big deal. You'd want to do it from the interior of the car. With the top up, behind the rear seat there's a sheet of vynil that hides the top hydraulics. This is attached with a few screws and comes-off quite easily. You'll then see the rear of the trunk compartment and how it's constructed out of flimsy plastic... it should be very easy to cut with a utility knife.
For my car however, I already took out the rear seat and I replaced it with some nice covered fiberboard for a finished look. I'm just going to mount a couple of 10" or 12" subs right there where the back seat used to be. These would obviously have to be free air subs or a custom enclosure would have to be built. Either way, the subs are now in the car's interior and I'll be able to take advantage of that as best as I can!
Let me know what you do and how it works out!
Good Luck!
-John