Kepler:
Your questions are all good and legitimate. You have correctly noted that scriptures are used to support pre-existing doctrine, not the other way around, as supposedly Charles Russell sought to understand them. I was raised a good JW and wondered myself about the clear and obvious discrepancy b/w how JWs view the fulfillment of prophecy re Babylon's destruction and the actual, historical events. I believe that one way around this problem is that they claim that Bablylon "fell" from a spiritual standpoint when the Israelites were freed and able to return to Jerusalem. That is, it was a spiritual/metaphoric "destruction" in that Babylon no longer had dominion over God's people. Of course, that completely misses the point that the prophecies unquestionably pertain to a sudden and very violent overthrow--old men, young, virgins and babies all being run through with the sword, etc.--and that such violence would be at the hands of the Medes.
By all means, assemble your questions and send them in to the WT. And please keep us informed as to the response. My prediction is that it will be several months b/f you hear back and then, at best, you will get a response patchworked from various WT articles of varying age, glossing over your central concerns and focusing on how wonderful JWs are and how amazing the preaching work is and how incredible the hope of the new world will be.
Still I could be wrong. But please, share it with us. And good luck!