Huge loss of bass after adding hardtop to the Jeep

[Mike4068]

So I had a fastback soft top on my wrangler and my sub was amazing. You could hear it inside of the factory that I work at. The change in the cup holder looked like a popcorn machine and the wipers bounced off the windshield. I put a factory hardtop on and now the change in the cup holder does not move and the wipers stay flat against the windshield. It's barely audible inside my work. The hardtop adds space above and behind the roll cage that the soft top didn't have. Could this extra space be causing quarter wave cancelation? Does anyone have any suggestions on how to combat this? I have a Fi sp4+ 18 running on a Rockford fosgate t2500-1bdcp in a ported box tuned to 30hz. The box takes up all of the area behind the front seats and I can not redirection it. The sub sits behind the passenger seat and the port is behind the drivers seat. My once mighty system now sounds like a 500 watt Wal mart garbage special. Any guidance would be greatly appreciated. I have been trying to research this but I can't find anything relevant to this particular scenario.