Done. I've learned a lot since I wrote that and I hope this helps someone. Don't change all of your tags yet!
After experimentation I recommend the following to anyone having trouble with media scanning. Put your micro sd card in and do a scan. Leave it alone! It may seem like it locks up, and it is definitely taking longer than it should, but eventually it will clear. Once done, look at your files, in my case they are all shown as "null" and cannot be accessed via "all music" or file directory view.
Do a factory reset. After this, every time, all music is still hosed...but now you can go to directory view and select a song from any folder you have. Once you do that it will do a quick scan of all the songs in that folder, and they will all work correctly and show in "all music" etc. At least I can use it now...but I have over 500 folders....doing them one at a time does not sound like fun.
My other issue is that the DX90 will occasionally not show correctly in usb connect mode. It shows the internal memory and the sd card as removable drives, but in the case of the sd card it does not recognize the drive size or label. Usually dismounting and remounting will fix this, or another factory reset.
Thanks for your research. You must be a very patient person! I will prepare myself for this.