Msi g97 gaming 7 gets stuck on 99 and more

I am not shure where to start. I'll spare you the entire history of my problems just ask if you want to know it.
Right now I have the problem that my boot time is very high. The Motherboard gets stuck at code 99 (super IO initialisation) for about 60 seconds before it boots regularly. Also (since I have selected disabled in the super IO configuration) it's getting stuck at 9c (which is the USB initialisation). This is a lot of time, considering the 25 sec boot time I had under Windows 7 with my RAID 0 SSDs.
When the system is running, various USB ports don't work.

i7 4770k @ stock
MSI Z97 gaming 7
ubuntu 14.04 (gnome, fresh install)
samsung sm951 M.2 SSD (trouble really started after installing this thing)

Thank you already for all the help.

sounds weird, did you allready try a bios update?

Yes, I have flashed the BIOS. Before I flashed it the SSD could not boot the Ubuntu OS.
I have now taken out the M.2 SSD and put a Windows 7 on a SATA SSD. The fast boot is back so I think that it is indeed a problem with the M.2 stuff.
Do you think I should put a Windows on the M.2 and it could change something?
Thank you anyway.

I would say give it a try.
If it also boots slow with a windows 7 installation on it, then atleast we can exclude some things out.
Maybe there is an issue with the Samsung sm951 M.2 SSD it self.

i´m currently trying to look if i can find anymore info on Msi user forums.
I think that the error code might be associated with m.2 storage device,
that the bios somehow does not detect the storage device very well.
Have you ever seen an A.2 error aswell?

I have reinstalled the M.2 SSD and the boot time (only change is the GPU from a 7950 to a Fury X) is now 18 seconds - which is very good.
Also the theme makes the top bar (of applications) now black and the entire system is not lagy any more.
Now there is only the problem with the USB ports. I've double checked in the BIOS - there is no option to disable USB 3.0 and all the ports that don't work (at least right now) are the 3.0 ports (which is all except 2). Yesterday I've had that different though.

Edit: I've not seen some of your stuff, sorry for that. I've never seen the A2 error so far. But I can tell you that 9C is super IO initialisation (disabled it in BIOS to get rid of getting stuck at that code) and 99 is USB initialisation. Which I don't think has to do with the M.2 SSD, since there is a separate code for SATA initialisation.

yeah 18 seconds for a cold boot sounds reasonable to me.
So i guess the m.2 issue might be solved.

But there is a USB issue now aswell?
Does your case has front USB ports?
If so then could you disconnect those.

Yes thats A2 if im right.
Atleast thats what they talk about on the msi forums.
I dont have a full list of error codes from Msi board myself, but i could look it up later today.

The USB issue has been there since the beginning of this operation. Typically it's not a good idea if I throw all of the problems out at once.
Because my writing is so inefficient people are usually overwhelmed by the length of the post, so I decided to split it up.
I've done what you have recommended and unplugged the front ports. They were working despite being USB3.0 (now of course they don't as they are not plugged in any more).
If you'd like to have a full list of the boot codes you can look at the manual, page 33. They are not all super detailed, but they are there.
Look here:
Thank you for the help. (yeah, I know I sound like a broken record, but I had no idea what to do, if no one would care - which has happened in the past)

the reasoning behind unplugging the front usb ports.
somethimes those ports getting damaged trying to short the board.
Then you could run into strange issues according to failing usb ports and what not.
Since your front ports were working fine, it does not seem to be your problem.
Basicly your could re-connect them again.

Still all those issues shouldn´t basicly be happening.
I have a bad feeling that you might endup with RMA´ing this board to Msi.

I'm not sure how to say this. I'd be so happy, if I just had one single easy problem with PCs in my life.
Of the nine mainboards I had I RMAed eight - if you count this MSI board in as well.
Not because they would not post (well one had that sometimes), but because they were installable when the ethernet was connected or when I had more then one SATA storage device connected. One of them would give me an error of one of my SSDs in a RAID and take two tries to launch. An now one would not give me the USB Ports.
Well the "working" motherboard also has to try a few times to boot - but that's the best I had with fife RMAs and not just Foxcon mainboards. I had three Crosshair V Formulas and two 990FX A UD3s.
Fortunately I don't have to go via MSI for the RMA. The shop does that and I never had an issue (except that it sometimes takes two months) there.
Probably I can also get an other mainboard for it - now that Skylake is out.
I'll ask them once the Fury X Crossfire testing is done.
Thank you for your help.

The only thing you could try, is taking the motherboard out of the case.
Lay it on its box, connect everything, and try to boot it up outside the case.
Could be that there is some kind of an issue with your case.

Can't really think about that - since my mainboards have died inside three different cases, but thank you anyway.
It's pretty late over here, so excuse me if I am short on words.

No problem, i know it can be realy frustrating.
Still weird that you have soo manny issues with boards.

Almost forgot that thing.
Well, it's a lot less frustrating, if you have 2 backup PCs.
If you have any idea what could give me all the DOA mobos, let me know.
I know that I am probably not that safe with only grounding the cases of my PCs, when I'm building on them.
But since the only two PCs without problems I've ever built for me were built without grounding at all I don't think that's a big deal.
Btw. How familiar are you with strange boot sequences?
I have an other problem. It is nothing that I need to have fixed, but since I am talking with someone that appears intelligent, I might ask anyway.