I removed all SCSI and plugged in an IDE hard drive and CD drive to verify my thoughts that the SCSI card was having problems with the new system. Nope - lockups kept happening, and even more frequently than before. The new hardware is going back to Fry's.
I'm back to the old motherboard and reinstalling everything. I put my userID and password in the eCS Maint Tool and it's not able to fetch the FTP account. I suspect the new eCS site broke something. At least I'd already set aside all the updates so I don't have to download them again.