So over the various years of upgrading my computers. I would always take the main HDD out of the old one and put it into the new one without reformatting. So I have 3 Windows folders, one on each HDD. Should i only have one?
yes, that is a bad thing. Actually, when you change motherboards you need to back up any data you need saved and do a fresh installation on the new system since most likely the hardware on the motherboard is totally different then the previous.