Ok, since my last post I finally decided to poke around in the physical part of the PC and moved the GPU to the secondary PCIE slot, which seems to have alleviated the worst, game breaking latency. Though I never ran a trace with old GPU (which I had in the primary PCIE (3.0) slot) I would say the performance right now seems to be on the same levels as then, maybe slightly worse but bearable. There are however still underlying latency issues with occasional multisecond spikes (accompanied by a "BRRRRR" sound), occuring maybe a handful of times during a days use. Those seem to happen when starting new applications/processes. There are also more lowkey latency, primarily discernable while playing and a pop every once in a while.
If possible I would be very grateful for further help with this issue. I have uploaded a new trace below (post-PCIE slot change):
Dropbox - CPUhmm.7z