All good points above. So your chipset drivers are definitely up to date I assume.
 
In regards to mix control was it a clean install or an upgrade from a previous version. If an upgrade I would uninstall/reboot and then install the latest version. I am assuming you are using the ASIO driver.
 
Yes please check out Intel Speedsteep and core parking (which is a registry hack).
 
After you've used latency monitor another good tool is this one:
https://technet.microsoft.com/en-us/library/bb896645.aspx
 
I would strongly recommend using the LAN port onboard the motherboard rather than USB. You can right click and disable it if necessary you don't need to unplug the cable (it's actually better that way).
 
Last very last thing to try is a separate display adapter if you have one lying around, I much prefer them to internals to be honest.
 
All good advise above esp about USB ports...

I was having issues with my wireless mouse & keyboard.
The dongle was plugged into the back of my machine because I only have one USB port on the front.
As a result, the kbd/mouse couldn't "see" the dongle, so I bought a cheap little 4 port USB hub to go in the front port.
Problem solved.

I just built an almost identical system and not only that I also use the 6i6. 
 
I kept getting blue screens so followed the typical troubleshooting endless loop of fixes, updates and head scratching. It's running great now once I found the problem. So don't rule out the hardware on a new build. I even bought more memory. 
The cause= Power Supply see below. 
 
Gigabyte Z97X-SOC ATX LGA1150 Z97 DDR3 PCI-E16 PCI-E8 XFIRE
Intel Core i5 I5-4460 Haswell 3.2GHZ Processor LGA1150 6MB Cache 
Patriot Viper 3 8GB 4X4GB PC3-12800 DDR3-1600 10-10-10-27 1.5V  16 Gigs RAM 
Samsung 840 EVO Series MZ-7TE120BW 120GB 2.5in SATA III Internal SSD Single Unit
OS drive - Run the EVO performance restoration app. 
Western Digital Caviar Blue 1TB SATA 6GB/S 7200RPM 64MB Cache 3.5IN  
Cooler Master HAF 912 Combat ATX Mid Tower Case Black 4X5.25 1X3.5 6X3.5INT 4X2.
Cooler Master Extreme 2 Power Plus 725W ATX   
 
I swapped out the Cooler Master for a Sparkle I bought locally and all is good now. Bummer is I returned the faulty power supply and they sent me a new one! I now do not trust Cooler Master so it's sitting on the shelf. It's sort of like my fear of Behringer, once burned you loose me forever.  
 
And for sure run Latency Mon.  a must do to test all new systems. 
For sure disable the pesky Video card audio driver ( I think that's what Craigs link goes too) 
For sure run msconfig and nuke all but micro soft apps ( see check box)  that are set to run on startup. 
SSD drives often have firmware updates that are not covered by Windows update service. 
 
And as a matter of course I plug the 6i6 into the back usb 2.0 ports. USB 3.0 ports are Blue so use the Black USB 2.0 ports as there can be issues with some USB 3 ports. Not all but some. Focusrite fixed the issue with driver 1.8 but I still would avoid USB 3.0. 
 
FYI I run at 44.1 or 48 , 24 bit. and set the buffers at 7-10 ms for most recording and mixing. 
I find below 7 ms with a large project it is unstable. So I use 10ms mostly and never have issues. 
The Scarletts are not stellar at low latency. For that buy an RME. You might have better luck with your i7 processor but finding the sweet spot for your buffers is important. 
 

Scarletts should run perfectly well with this configuration (I have no idea though whether it can or cannot handle USB 3, you might want to contact Focusrite for their recommendations)...

To be honest I've probably built 1000+ machines in the past, however once I got bitten when building my own PC (an incompatibility with display adapter and motherboard, which neither vendor would swap out) and I realised it was better to go to a vendor like Dell or HP, you get much better support....You don't need a custom built powerhouse to record music nowadays, and even vendors supply powerful workstations if you really need or want the power for some reason (check HP's Z range).
 
With dropouts I would be looking towards software and driver issues.

Anyway on with the OP's issue..
 
One thing I would like clarification on after the OP's taken everybodies advice, this really is the smoking gun everybody should consider (his spikes happen during playback/recording):
"the audio system starts cutting out and finally stops or crashes"
 
What does "crashes" mean can you be more specific?

Built a new system not a lot different from what you have too, and also using a focusrite. Did all the updates for software and hardware and had similiar issues to you. After a lot of frustration and heartache, it turned out to be the USB ports. I was running both 2.0 and 3.0 to the front of the case, and had 2.0 and 3.0 ports on the rear off the motherboard. I noticed it made a difference changing things around between the different ports, but still kept having problems, so ordered a PCI card with 2.0 ports only. I now run the interface from the card, and run all my other usb stuff from the MB ports and havn't had any trouble since. That was through X3 and now Platinum. Hope you get it sorted. I remember the pain.....

Bristol_Jonesey
I was having issues with my wireless mouse & keyboard.
The dongle was plugged into the back of my machine because I only have one USB port on the front.
As a result, the kbd/mouse couldn't "see" the dongle, so I bought a cheap little 4 port USB hub to go in the front port.

I also had problems, especially within Sonar for some reason.  I have sufficient ports for other things, so I just ran a USB extension cable to bring the dongle close to my mouse.

Similar problems (now solved, as follows) here, too: along with all the other possible solutions, add this one:  you are accidentally using a 32 bit VST or plugin in a 64 bit system.    Caused very similar symptoms to what you describe.  Search out where vsts are installed, make sure the 64 bits are distinguished from the 32 bits, and delete (or save away in some non-accessed folder) the 32 bit ones where a 64 bit exists.   
 
A whole lot easier to try than re-installing windows, re-installing sonar, updating drivers, etc etc, which was the advice I (and you) received ....

JL81283
and the processor scheduling is set for Background Services.

That could be the whole problem right there. This is a long-discredited tweak:
 
http://forum.cakewalk.com/FindPost/1239881
 
My personal experience with it on a couple of different PCs back in the XP era ranged from no improvement to having the O/S come to a grinding halt when I launched SONAR.
 

williamcopper
Similar problems (now solved, as follows) here, too: along with all the other possible solutions, add this one:  you are accidentally using a 32 bit VST or plugin in a 64 bit system.    Caused very similar symptoms to what you describe.  Search out where vsts are installed, make sure the 64 bits are distinguished from the 32 bits, and delete (or save away in some non-accessed folder) the 32 bit ones where a 64 bit exists.

It seems very unlikely that the mere existence of 32 bit plugins would cause a system to have playback problems. If you're not using the plugins, they should have no effect.
 
Anyway, I have almost exactly the same setup as the original poster - same interface, OS, CPU, memory - and it's running like a dream. I'd be interested to know which background tasks are running in this situation. And I assume this is happening with the USB network device completely unplugged? (Networking over USB is usually a bad idea for performance, partly because it has to interrupt the CPU so often.)

Trouble is with this kind of situation there are so many possible causes and fixes...

So here's another one to try. The good news is it will only take a few seconds.

Open Sonar and go into preferences. Check the "advanced" button at the bottom. One of the menu choices that appears will be to do with the configuration files, also known as the aud.ini file. Tell Sonar to create a new one (it will rename the old one and keep it as a backup). If aud.ini wasn't properly created in the first place it can cause all kinds of problems.

And another....

Go into the BIOS amd switch off all the cpu CE state power management stuff. All of it. Also "turbo boost' if present. Then google "turn off windows 7 8 cpu parking". Which should find you a registry setting that needs altering (if I remember rightly it needs changing from 64 to 0) to stop Windows putting cpu cores to sleep. Core parking is meant to reduce power consumption by "parking" cores until the system load indicates they are needed. This won't affect most things PCs are used for in the slightest, but it's lethal if you want a DAW to handle near real time audio (which is exactly what you do want). I've seen core parking bring my DAW to its knees, with 80%+ on two of the 8 virtual cores causing stuttering and dropouts while the other 6 were still parked because as far as Windows is concerned that's the greenest way to schedule the cores so it does.

Finally, run the pci bus latency checker as has already been suggested. If it finds a problem (usually wireless networking), solve the problem.

Other than that there's very little do tweak or adjust on a Win8.1 PC for audio use. Most of the pre-Win8 PC tuning tips are no longer required and some are now counter-productive. My DAW also runs Photoshop (a fast PC configured for DAW use is usually also very fast at processing graphics and video) and even has a few games installed for when I need to take a break and do something else for a bit. Plus a copy of itunes and a few other things, and it runs Sonar very well indeed despite having the kind of number of background processes running that would have been unthinkable on a DAW a few years ago.