Not sure but by sealing things up you have changed the volume of air in the passenger compartment.  The air in this cavity has natural frequencies that can be excited by exhaust or other sources and you have effectively changed the volume.  The muffler itself becomes a speaker - think of the surface area times just a little vibration and it becomes a speaker at certain car or engine speeds.  It can excite floor panels giving you even bigger speakers. You may have discovered one of the many Murphy's laws of resonance - attempts at solving a problem often make the situation worse.  Un-do the last two steps and see if you return to "normal".  Could be that allowing some air transfer between the passenger compartment and the trunk will de-tune the drone.  If the drone goes away with window open, this tends to support the acoustic resonance condition as this produces a large change in volume.  You cannot eliminate acoustic natural frequencies just like you can't eliminate structural natural frequencies.  What you can do is try to separate the forcing frequencies from the natural frequencies to avoid resonance or tune the system to produce potential droning at speeds you normally would not drive.  As you may have found, it is often easier to move natural frequencies right on top of forcing frequencies than it is to move them away - Murphy.

I can't claim extensive on the noise part - there is a fair amount of art with the science and that comes with years of experience and my focus has been on the vibration side.  With aftermarket exhaust you are often dealing with less than ideal hangers depending on who did the install and how it was adapted to fit.  I was just trying yesterday to find some links that I thought Steve had posted on the use of late model hangers for even better decoupling - or he showed me the hangers when I was looking at his car up on the lift so my memory may be playing tricks.  You may also look into dropping the mufflers down 1/2 to 1" further away from the body if you can swing it.  The increased distance between the speaker (muffler surface) and the floor panels may help.  Check all other hangers to make sure that nothing is in contact or too stiff.  A lot of the universal straps and hangers are very stiff from a noise transfer perspective.  Another potential source of unwanted noise and vibration is the exhaust system structure itself.  In my car's history I did a 6 cylinder to V8 swap and installed headers and had a local shop fab the exhaust.  I ened up with a natural frequency of the header to muffler section that was excited by the driveshaft at 49 MPH.  The driveshaft was bent and I replaced it but still at 49 you could hear it and feel it because natural frequencies only take a small amount of excitation to produce amplification.

I have never looked into the drone issue but it seems to be more of a transmitted noise condition from the exhaust system into the floor than the noise coming out of the pipes but this is only a guess.  When swapping to a more free flowing muffler you are not only getting more noise out the back but the muffler casing may also be more reactive than a nice heavy stock muffler.  I am sure others have studied this but if there was a great solution it seems like it would be well publicized.  The passenger cavity seems to be ideally sized to magnify this noise so that is not so easily changed.  It seems like you are on the right track with damping matts, etc.  I will ponder a bit more and see if I have any more thoughts.  If I ever get my car on the road again the solution will be to only drive it when the top is down!  Not so easy to do in a closed car.