TokenAndPermUserStore Clear decreases CPU usage for a short period of time
Than you all for your time and effort in finding a solution. Especially @David Browne - Microsoft since he was correct by letting me know that we should patch.
We had a meeting with the dba's, the application owners and the technical team of the application vendor.
In this meeting it came to light that the same issue is present for the other clients that the vendor has, due to the nature of the application and its code.
Similar to this.
The solution that has helped their other clients with this issue, is to upgrade to SQL Server 2014 CU7 or SP3, which we will be doing as soon as possible (SP3 preferably), which should put an end to the 'tokenandpermuserstore' issues.