Well, I'd start with a sheet of plywood, a table saw and some Elmers glue . . .
Haha, just kidding, I've been thinking about the same thing under the seat of my '46 where the gas tank used to be. The only thing I can think is to make the box shallow and point the woofers right up your *$$. Other than that, I'd say the only option is to find a seat that's a little taller.