Sorry, I repeated some things you have already done...I was on a mobile so it was hard to navigate.
I disabled some services while trying to solve the same issue on a toshiba laptop.
Try stopping and disabling the following services in services.msc.
-superfetch
-application experience
-windows search
These do not affect the normal usage... web,networking, etc. killing superfetch helped me a lot.
I am thinking disk access here since you had a pop while opening a program but the CPU spikes then as well.
I also set a bunch of services to 'manual' but the list is too extensive to list here .
Have a look at blackviper.com for your OS for some more suggestions about which services you can safely kill.
If you have the ability to switch the firewire driver to legacy mode, try that. just google "firewire legacy driver".
This is a must on my Tascam firewire interface and many others.
Just as a check, make sure your HDD controller is set to DMA mode. google " setting HDD DMA mode".
I am running dry here, and if none of this works, I starting to think maybe you can't get there from here.