The stutter effect looks like audio interface drivers. Make sure you are on the latest including the firmware.
My advice in full....
1. Full backup
2. Turn on your firewall permanently and scan for viruses and spyware. If you've been on the internet at any stage (using browser or not )without a firewall you have been put at risk.
3. Run windows update several times including optional updates, that should sort out any c++ stuff anyway (although we have not seen any c++ related error so I'm scetptical ). It should also improve performance and reliability.
4. Install X3E. Make sure the plugins installed are on the latest patches. Perform a VST reset afterwards followed by a rescan.
5. Get the latest drivers for everything. Run 'Intel autoupdate' assuming your machine is Intel based. Make sure you are also on the latest firmware (esp your interface).
6. Reconsider about being always off the internet there really is no benefit nowadays. We seem to get a lot of people who have issues who are off the internet nowadays. You can always disable the network adapter whilst recording anyway.
7. Run chkdsk and defrag.
8. Consider disabling Intel speed step (assuming it is on).
It just might be that now is the time to reinstall windows on a clean partition.This really looks like a system config issue rather than Sonar. However I suspect it's a result of some system component not being up to date or a rogue or unwanted process. You could also check the windows event viewer for errors.
Also with that many DAW's running (I suspect you are running a lot of software) you might want to be looking at a deeper level. That is disabling process and services you don't need that will interfere.
I would recommend a sequential approach anyway as above.
Cheers.