Mounted pump and radiator, hooked up USB wire to header on mother board and fan header to cpu1, 2, and AUX fan. Went to Bios and set all fans headers to 100% that i plugged into. Pump is going and fans are at 100% RPM. But i dont see the clc under USB's in Device Manager and software keeps saying it cant find the cooler. i know the usb are working with flash drives, and headphones so it cant be the header. ALso the LED is not lit. 
MOBO evga x299 micro atx 2
EVGA CLC 360
 

Hello,
 
LOVED this reply!  Good stuff keeping a level head & positive outlook despite having what I know is a frustrating issue.  I am surprised someone hasn't jumped in here and tried to help as of yet.  I have the same cooler but it is new in its box awaiting my final parts (come on X570 Dark!!).
 
This may be a longshot (sounds like you have checked most of the main things) but if you are running a Windows OS have you checked in Device Manager and looked for any "unknown" or other hardware that you do not recognize?  I recall going back & forth with a couple AIO CLC's (not EVGA!) and the end cause was they were showing up as unknown devices and therefore not showing up under the software. 
 
I see this post is about a week old.  If things are not working 100% I would recommend reaching out to EVGA directly for assistance.  Hoping it gets sorted if it has not all ready!!

Oof, hope I don't have the same troubles... Throwing this on an 11600k in a z590 board.

Okay so I plugged the fans into the wire that came with the cooler labeled "fans" and the "motherboard" cable to the aio header with the USB cable to a USB header next to the front input one. I started up the Flow EVGA software and set the pump to 100% and fans to auto. No problems. Did you try swapping the USB headers?

Interesting

I've been away from this forum for a while so I just saw this. (been waiting for a graphics card)
 
I'm probably missing something but I could swear the OP didn't say what the pump was plugged into. It looks like the fans are individually plugged into 3 separate fan headers. The pump is connected to the usb header. So what is powering the pump?
He says the pump is running but I don't see how.
 
Usb does not power the CLC360. There is a pump power cable for that. The usb is only for communication. It is not required to run the clc.
I apologize in advance if I'm wrong but please explain how I'm wrong.

Correct. But if the pump has no power then there will be nothing to recognize.
I'm just trying to figure out why the OP couldn't see his pump.
 
Unless I'm reading it wrong he didn't mention connecting the pump power cable. Could be he just didn't mention it.
 
There are two cables coming out of the pump (not counting the usb port). One goes to the motherboard to any fan header or pump header. That's the pump power cable. The other can go to the fans if you want. I left it disconnected and plugged the 3 fans into a splitter and that into the CPU1 fan header. But I arranged my cables so that I could switch the fans to the pump connection for later testing.
 
I ran the pump power connection through a fan cable extension all the way down behind the motherboard and around to the pump header on the mb. That way if I end up changing and powering the fans from the pump I'll have more then enough power since the Z590 FTW pump header is rated at 3A. Yes, I know, the fan headers can supply 2A (which is also plenty) but I thought I'd use the pump header.
 
This is how crazy I was getting waiting 3 months for a graphics card!
 
This unit will function without the usb connection. The usb is only to allow the motherboard and software to recognize it.
 
Edit: after all that I forgot to add that I also connected the usb cable, again for testing purposes.