I'm guessing that, like you said, the eMMC has died or failed in some way.
One last suggestion I can come up with is that I can send you a copy of -my- working RootFS and OptFS images, and you can try flashing the RootFS with the Flasher, booting into my tool(doesn't require OptFS to boot that far), and flash OptFS through that.
This has a chance of working, but is in no way guaranteed.

If this fails, you are going to have to look into alternate/custom OS stuff - Think mounting your RootFS image, editing /etc/fstab, and changing the /opt/ partition from the eMMC to a partition on the SD card.
As the RootFS is still intact, you can probably do this and get your N900 working again this way, but you may have lost part, or all, of the eMMC.