Have you installed all drivers, including Intel ME windows drivers and firmware? I have heard of slow POST times when there is a memory issue, so install all drivers, set BIOS to defaults (for now) and see if that helps...
I have to go to bed soon, but a video might help. I suggest that you go to the motherboard support page and download every driver and firmware update. That will make sure that you have all of the latest versions. It sounds as if you can boot into Windows at least, so that is good. Take it slowly and hopefully the startup delay will be resolved... I do not have the 790 board, but I will try to make some helpful suggestions...
If you are using the drivers on the USB stick, some of those might be out of date.
It might help to provide the time it takes to start up. Then other people with 790 boards can see how that compares.
I have the 690 Hero which takes about 35 seconds until it gets to code A0 on the LED display. By 43 seconds it reaches the Windows login screen.
OK, well that doesn't seem too crazy based on my own experience. So going back to your original question, I think that it's normal and nothing to worry about. I can also hear fans spinning up and slowing down when my PC starts. I can't comment on the CPU fan as I have an AOI that makes very little noise and I can't say which other fans speed up and slow down without looking very carefully, but again I think this is normal and all part of the ASUS POST process. No two systems are going to be exactly the same.
If everything is working in Windows OK then I think you're all good. It's also normal for many monitors to turn on after a while because they are searching for a signal. My main monitor takes a while to sort itself out as well.
My setup has the same behavior. Two boots for every boot is not normal. Not only the fans stop. I can hear the "click" that came from PSU indicating the shutdown between the two weird stages.