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Thanks for the reply!
Just to be clear, I used win32diskimager to write the initial image to the MicroSD. It was after setting up my controllers, configurations, etc. that I made the image with HDD Raw Copy.
I also have a 2a 5v power supply. Sucker cost me $13, but I’ve had issues with lesser ones.
The USB transfer was the last thing that I tried, and it did corrupt the card, but so did samba and ssh.
I found a 4gb MicroSD card and I’m going to try that one from scratch. It won’t hold all the ROMs, but it will be a good test.