You can use something like HWMonitor to check your actual CPU clock.
 
I'd start by stripping the machine down to the barest of essentials.
Measure your DPC Latency.
If you've disabled everything possible... and eliminated all other variables, the bottom line is the motherboard will need swapped.  That sounds like a pain, but compared to what you've been thru... it's really not that big of a deal. 

on some boards from ASUS...M.2 if selected, defeats or hampers TB...
 
So you have to do the homework and read the instructions and manuals properly...for I cannot read into it for you, nor will all here for you.
 
You have to go slow...read, understand what you are reading into...and proceed with caution...
 
If you are using M.2 with TB and firewire and usb..and and and...you are going to get odd noises!
 
So make up the mind...what port you wish to use...and look into how to employ it proper....first read the readme files...
and Manuals..for your system setup, irq's sharing...and make all redundant devices disabled....How you do that, is either by Bois setup proper, or through windows Device management.
 
Device manager /Power settings needs be tweaked, turn off all sleep mode, and monitor sleep, ..and no idol sleep on drives....and such setups can be set...to gain maximum performance of the system you have to tweak it for what you want it to do, with what you need for it to be done..and all parts sorted to get that.
 
Turn off system sounds.
Go into device manager systems, and make sure USB ports are set to not let windows turn this port off....((power management)) it is, but in a different part of the System page...device/systems/usb hubs...
 
And if you wish..another setting is to run in background mode, or program mode...but some say is dependent on what you need done.
 
 HDMI audio might be tweaked to be turned off...it does help to do that....I found.
 
The cpu parking must be tweaked to off...using Cmd prompt.in admin form.
 and set the cpu limit to 100% in that power tweaking session...might also help?
 
 
So you have home work to do on M.2...and your Mother board working with Firewire, and TB?.....and think about firewire or TB..but not both at the same time working...with m.2 Perhaps?
 
conflicts of irq's sought and told...what is in conflict must be showing up in the performance tab, or system info, or remote viewer for any issues....Right?
 
cheers

Oh...forgot this...Power of conditioning...It may be a good idea to get a UPS with some sort of filtering!!!
 
You see, when the heating or air conditioner goes on...(in my house here) a spike is created on the lines of my circuit boards breaker system...and I get noise through electrical back lash.
 
So, that might also be put into the mayhem to solve...asap.
 
For a good system, has backup systems employed....if the power goes off...or spikes occur...You can rest a bit more sound in safely turning off your computer and saving your works done..in a time alarming way, ...best to be safe.
 
As i did employ this method early on in my studio build....IT DID SAVE MY BUT, AND..LESS NOISE...YAH!