A week has passed and my n900 has been stable and steady again, even with overclocking. It was something in the partitioning of the internal flash, for sure.
I advice those who suffer the same problems to:
1) backup the /home/user/MyDocs directory, including the hidden directories (e.g. .documents, .images, .videos
2) backup your personal stuff with the stock backup utility
3) reflash rootfs and emmc
4) reload everything from your backups.