had two baja's ('64 and a '67) - neither had rear seats (just a plywood platform) - both had roll cages - so if I'd wanted to build a sub-woofer box it'd have been pretty simple (I didn't - you would have never been able to hear the radio over the open headers
) however - if you've got a back seat still in place try the "hole" between the back seat and the rear window - should be pretty simple to fabricate just a "lid" that'd hold the speakers and seal it up pretty well -