First I would try copying the files again. You will get the file missing message if the file is corrupt. If that is the case you may get that message for a couple of other system files as it looks for them when booting.

Also could be an issue while copying the files. Laptop drives are usually set to Device 0 by default. So you could have issues if you have another device on the same cable, no matter the position, if you don't jumper them correctly.

I haven't read the article but I believe the reason for FAT32 partition is so that it can be read and written to from a standard DOS.