What sub did you use? Qts of the sub, and the resulting system Q can make a big difference...

And I can't stress enough how important it is to seal the back wave from the front wave. Failure here will kill you bass. This means plugging holes, filling hollow structural members (they often have holes both in the trunk and in the passenger compartment, which will allow the waves to mix). Unless you put a lot of work into it, I will bet that was part of your problem...especially with your pass through. A common misconception is that IB setups are easier than box setups, and that's just not true.

I'll throw my lex on the meter one day, but its far from 'quiet' or 'bassless'

Toby