The 512 proto motherboards would have a paper label saying "Mac 512" and the RAM would have had a factory look of soldering. The label can easily go missing but the RAM would not look like it was added later. As for the floppy, if its original to the Prototype then it may still have a date on the side of the drive. It has to be taken out of the cage of course. But an easier way is to look in front and to the bottom right. It will should have a capacitor laying on its side. This was part of the original modification by Sony to get them into specs set by Apple. There are a couple other minor changes too. I took a pic to show what I mean by the capacitor.
The case frame would also end in a "-A" or "-B" with "-B" being production run on the early Macs.
The ROMs would not end in "-A" or "-B", original ROMs were just 342-0220/342-0221 including early production units.