I am unsure about the motherboard at the moment. The case has 3 fans and I chose the motherboard because of the fan connectors. Will the fans work with just one connector or will I need a connector for each?
Yes it will. It will in all likelihood be the last upgrade you can do on this system as you can't run AMD's newer chips on that old chipset motherboard. If you can still find PII 980's or a X6 1100T then by all means. Maybe try looking at AMD's 9XX mobo's, 970/980/990, at least that way you can move on to Bull dozer or Piledriver.