I just wanted to put some closure on this problem, as I gave the full sync another try last night with a stock kernel and init. Indeed, the 15 gigabyte sync went off flawlessly. So the only question remaining is if it was the fault of not having enough memory because of user apps, or if it was something with the Hijack kernel. I don't know how to further narrow it down without risking corrupting my music partitions some more... But I guess my gameplan now is whenever I have a huge sync to do (not very often, of course) I'll just back out to a stock kernel, change the init, do the sync, and switch back. A little painful, but it's a workaround.

I'll wait until Mark Lord appears around here again to begin asking questions about what might be actually happening here.