The next step would probably be to graduate from Safe Mode to Safe Mode with Networking and make sure that the problem was not present.
Then I think I would use Safe Mode to configure my machine for a Clean Boot
https://support.microsoft.com/en-us/kb/929135
Easily done, easily undone.
Basically you're just disabling all the Startup Items and All
non-Microsoft services.
Be sure to check the box to hide Microsoft Services, as you don't want to accidentally disable any of those.
After configuring your machine to Clean Boot, if that seems to provide any relief from the problem you will then have to take some time and determine what the offending program, service / process might be.
Carefully and deliberately one non-Microsoft service at a time or in very small groups re-enable them, rebooting after each change to observe any changes. Then graduate to the Startup items again rebooting after each change.
Understanding that in some cases, a Startup item may have a non-microsoft service associated with it and as a result you may not notice the impact until both the Startup item and the service are re-enabled.