That's a lot of things to change, so I wonder which one 'fixed' it?
I believe something with the logic board and/or RAM corrupted the hard drive.
I did try the 128MB EDO in the replaced board, and I started getting some glitches happening (Finder complaining about running out of memory, when nothing was running).
So, I think it was a combination of the logic board corrupted the disk driver on the drive, together with a corrupt OS (due to disk read/write corruption), and Mac OS 8.1 not having enough RAM for what I was trying to do.
I started with Steps 1-4 above one at a time, until the issues were resolved. The 1-4 are the order I went through, while testing in-between.