Seems like you have been very thorough so far in your quest to find the root cause of your issue! 
What I would recommend is to look at the problem from the angle that another app or process outside the sim might be causing the issue. You could open the task manager and let it run on a second monitor or run the sim in windowed mode with the task manager up on the main screen. If you click on the left to show the running processes and then click on the top of the CPU column it will then display the apps/processes taking up the most CPU cycles from highest to lowest. Run the sim and see if there is a particular app/process that jumps close to the top of the list consistently when you see the lag.