Unreasonably LONG Boot Time for unknown reason

If anyone is interested, problem has been solved and it seems there were multiple overlapping issues.

The initial cause, believe it or not was these:
2x1TB Samsung 850 Pro SSD in Raid0
2x2TB Seagate SATA3 7200 RPM HDD in Raid0
2x4TB Western Digital 7200 RPM HDD in AHCI
2x6TB Seagate 7200 RPM HDD in AHCI
Along with the OS drive, which Win7 seems to hate by default and has to be tricked into accepting, an Intel 400GB 750 PCI-E SSD w/NVMe.

What happened was, I made the mistake of stuffing all the Hard Drives in at the same time and Raiding the 2 pairs, just after first boot, when I checked if Win7 was fine, instead of doing them sequentially, by company, type and size to let each set up in a boot/OS properly. What I didn't know at the time was stuffing in all these various drives at the same time caused some major driver install fail and/or no driver install. I didn't notice, because once booted it ran like a dream, giving me great benchtests and phenomenal encoding speeds.

I got my first reality check of FAIL on software install/update reboots. Boot times were literally taking 5-7+ minutes along with the occasional S.M.A.R.T. error, on brand new drives that on multiple disc diagnostics said the Drives were 100% good/healthy. After a couple days of struggling finally trying to see if it was just one bad swap slot and flipping drives around, I noticed that drivers were installing for them. I could have sworn I saw drivers install for them, but I have a bad habit of not really paying attention to driver installs, because I've never really had problems with that before. I did them sequentially all the drivers installed fresh or for the first time, so the 5-7 minute eternal boot was solved. Next problem that arose was my USB 3.0 and 3.1 ports were transferring at 10-30 MB/s instead of 150-400MB/s. I had The latest intel 3.0 and Asmedia 3.1 drivers, but it seems the original USB Root Hub got screwed. After reinstalling the Root Hub, the USBs were all fine. Next it seemed totally out of left field regardless of system load that the system would get severe lag or freeze up for a couple minutes on the most menial tasks like deleting, opening/closing very simple apps or simple folder moves within the same directory. I knew it couldn't be the clock, because even at 4.6, beating on it with a stick, trying to abuse it, running multiple heavy resource apps, it's temp wouldn't go passed 53-54C and even those temps weren't sustained for more than few second spikes on individual cores. Thus after a couple days of elongated google fishing, it seemed the older firmware and driver versions on the Intel PCI-E SSDs just sucked horribly bad, so much so that intel even opened FAQ topics about it. After The firmware and driver updates, so far so good it's running how I was expecting it to run, not just good benchtests and fast encodes.

Only thing left that I found odd was a flickering orange light on the mobo. I didn't notice it before, because it's literally hidden immediately below the Graphics Card circuit board. It's right below where SATA6G_12 is written and right on the edge of the mobo, it's very small and it literally looks like an active orange spark, that flickers nonstop, all the time. I understand leds on or off and colors, but a tiny flickering orange led????

If anyone knows what that flickering led is, I'd like to know, otherwise I do appreciate those of you whom at least tried to help.

You know, this ASUS RAMPAGE V EXTREME 3.1, literally has more frickin lights, than a damned Christmas tree. A bunch of which aren't bad lights, they're like plug/port/socket in use and/or activity lights. Supposedly, according to a tech from Digital Storm, it's an activity light. I kind of concur with that, because mobo "bad lights" are usually severe and normally have immediately noticeable hardware fail. I just ran a quick benchtest: http://www.3dmark.com/3dm11/10916596
That came out cherry, device manager says everything is healthy, HWMonitor and CrystalDisc look fine... So I'm kind of leaning towards basically if it ain't broken, don't fix it. Also, thnx for the array comment.