Thanks for those details. I think I've found a way to solve your noise problem.
I'm glad to see you are using the CAM software. Before going further please check that all the connections for the Kraken X62 system are done as its instructions say. That system PUMP unit has coming out of it (according to its manual) one major multi-headed cable, a second cable with up to four 4-pin fan male connectors on it, and a small socket on its side for the cable to the mobo USB2 header. On the rad fan cable, do not be confused by the pin counts. It is doing something that all hubs and splitters do because any mobo fan header (and apparently this applies to the Pump unit's design) can only deal with a speed signal coming back from ONE fan. (More than one fan's signal combined together makes it impossible to read the speed.) So on the several 4-pin male fan connectors on that cable from the pump unit to the rad fans, only the first one actually has all 4 pins. All the others omit Pin #3 so that those fans' signals cannot be connected back to the pump. This has NO impact on the ability to control the other fans' speeds. Thus in the CAM software you will not see separate speeds for both the rad fans. Only one will be shown, and we are to assume that the other (identical) fan also is running the same speed.
1. Both rad fans should be plugged into that fan cable from the pump, with one of them on the first connector that has all four of its pins. You can read the rad fans' speed in the CAM software.
2. The 3-pin female fan connector from the pump should be plugged into the CPU_FAN header. It should NOT go to the CPU_OPT/W_PUMP header at the top of your mobo, nor to the CHA_FAN3/W_PUMP at the bottom. IF you have it plugged in to the wrong header and change it, check in CAM to be sure it still is reading the pump speed correctly. (I'm thinking that, if you move this connection, the CAM software might already be looking at the wrong header and fail to pick up the change.) If CAM no longer "sees" the pump speed, you might have to un-install it and then re-install it so it can find the right speed signal. Note that the CAM software will show this to you correctly as the PUMP speed, even though the BIOS Setup display for your mobo will label this as the CPU Fan speed.
3. I will presume that you have the power cable from the pump plugged into a SATA power output from the PSU (otherwise it would not operate!), and that you have the USB2 cable attached so that CAM can communicate with the Kraken system.
That will ensure that the Kraken system operates as designed. Now, on to the other two fans. The pre-installed fans on that case are the FN V2 models which are of the older 3-pin design. If that type of fan is connected to a mobo CHA_FAN header using the newer PWM Mode to control fans, it can only operate at full speed all the time, which is what you describe.Those two case fans must be connected to a CHA_FAN header that can be configured to use the older DC Mode, and THIS is where I found the "tricky detail" in your mobo manual. See p. 85-86. For both of the CHA_FAN1 and 2 headers there is no mention of this Mode, and I bet that is where those two case fans are plugged in. BUT for the CHA_FAN3/W_PUMP header (and only this header) you CAN set it to use DC Mode. So for this header configure it in BIOS Setup to use the CHA_FAN3/CPU Optional setting (not Water Pump), DC Mode and the standard automatic control curve, then set it to use the common motherboard temperature sensor as its guide (not the sensor inside the CPU). Remember to SAVE and EXIT to save those settings. Now, how to connect those two fans to this single header? Buy a simple fan Splitter. (You may find it hard to get a 3-pin Splitter, but any4-pin Splitter will do the job just fine.) Something like this (4-pin)
https://www.newegg.com/Product/ProductList.aspx?Submit=ENE&DEPA=0&Order=BESTMATCH&Description=coboc+fan+splitter&N=-1&isNodeId=1
or this (3-pin)
https://www.newegg.com/Product/Product.aspx?Item=N82E16812423168&cm_re=coboc_fan_splitter-_-12-423-168-_-Product
Those items are NOT Hubs. Note the difference. The SPLITTER has only two types of "arms": one ends in a female fan connector to plug into the mobo header, and the others end in male connectors where you plug in your fans. A Hub (do NOT get one for this) also has a third arm type that must plug into a power output from the PSU.
If you arrange your two pre-installed case fans' connections this way they WILL be controlled automatically (using DC Mode) by that CHA_FAN3 header and will run more slowly and quietly. There is no need to have them run full speed for extra cooling your mobo does not need.