Mine has never been flaky. (Stable under OS 9 & Debian, never used X on mine.) I'm going to guess it is the CPU card for the moment. Upgrades such as that are best removed and the machine returned to stock when checking other parts and then returned when all extensions and everything can be had and your environment is stable.

What I have found out is that normal USB -> 2.5 IDE cables are not sufficient for SSD's. My generic China adapter works fine on HDDs, but when I try a "fast" media, things go unreliably, unpredictably wrong on both reads and writes. However, this doesn't explain why your old HDD is messed up as well.