Ok, I finally got there! Thank God - I was beginning to think I was going to have to take it back to Verizon and claim I didn't know what happened to it. This whole thing is very strange, and I'm wondering why when I read that everyone else seems to get through this reflash process with no trouble.
So, as I mentioned before, on the first flash it got through flashing mbmloader, mbm, cdt.bin, lbl, logo.bin, ebr, mbr, and devtree before failing on the system partition with the aforementioned size mismatch error. The phone was bricked at that point, so with nothing to lose I edited the XML file to take out the first 12 steps, so that on the next pass it started with the system partition. RSD Lite hung up, and after 15 minutes I closed it out and rebooted the phone into AP Flash mode. I ran the flash again, and this time it flashed system and failed on boot.
I tried the same process again, and after several attempts and restarts of the phone and RSD, it passed boot, recovery, and cdrom before failing on preinstall (same error once again). After deleting the steps for boot, recovery, and cdrom from the XML it hung up on flashing preinstall and, once again, after several iterations of restarting phone and RSD it got through preinstall and radio, rebooted. The issues I had from uninstalling a couple of stock apps appear to be gone, and all my apps and customizations are still there.
What do you think about the reasons for all this weirdness? This phone is brand new - I just got it a little less than three weeks ago, and it shipped with 5.6.890 installed. Could something have been changed in the latest version of the Droid 3? Or maybe it has something to do with the latest version of RSD Lite (5.5)?
Thanks,
Mark