You only needed to apply your sound deadener to 25% of the a surface that you covered, but what is done is done. I would also be willing to bet that with all the curves that metal has from the press stamping done, that it does not resonate much. The outer door skin is what is resonating the most.
A 6" strip placed in the middle of the door horizontally, would help that tremendously. Also how is the bond between the brace in there? If that has aged, then the outer door skin will rattle against it and that is annoying.
you can use ABS plastic or plastic cutting boards to cut panels to seal off those holes in the door. You get need to get creative around the wire loom and door linkage.
You are on the right track about the Velcro and rubber idea. To say me typing I give you this link:
sounddeadenershowdown
A boatload of info in there, I have his product but have not done my doors yet, just the hatch area.
Curious about the rubber spray? you didn't plug your drain holes at the bottom of the door did you?