I don't have or use Prime. No matter what I order I get it's free shipping. And for Prime you remember their 2 day shipping? That's a crock. Never get 2 days. I once in a while use their trial. And never once got anything in 2 days. So without Prime I get shipment in the same amount of time that they say I would get with Prime. So I won't use their over price services. And don't care about their other benefits.
It has 2 fans, but they are optional. the other fan is under the cover on the top left of the mobo next to the Z79 on the I/O area.
I had the same board as the OP as well as the Z87 version I use as my Plex Server,
That fan is for the PLX switch chip if I'm not mistaken. A poor design choice just because they wanted to have that cover plate over the board, and without enough airflow, those chips run pretty hot. Most boards that used them would just have them heatsunk via a heatpipe that ran across the VRMs as well.
Glad you could find a replacement fan. For future reference, all the 4th pin on fans do is for PWM (aka speed control). You can plug 3 pin fans into 4 pin headers or 4 pin fans into 3 pin headers, the fan will just run at full speed. You can sometimes still control speed on 3 pin fans if the motherboard supports DC fan control (providing a voltage between 5V and 12V). But for a chipset fan covering the PLX chip I would just expect it to run a constant speed anyway so you probably could've just got whatever fan in the correct size.