Long and four short is hardware failure if I remember right
Long and three short is GPU failure
Not sure what's going on there exactly but it might be worth your while carefully unmounting everything and then setting up again...reseating connections and generally making sure everything is in place.
When you install win 7 you should only have the target disk plugged in, no others, otherwise windows writes some partitions to other drives and then things get complicated to boot if those drives go missing.
Lastly you should be able to set the BIOS to "ignore" low fan speed...but if your CPU fan is spinning that low I'd be looking into it. Maybe the system doesn't like low CPU fan speed and is halting?