After doing a clean install and running driver 6.3.20-4 everything is running quite smooth. The pen is still a bit to sensitive in some programs, but it is working ok. Updated to 6.3.20-8 yesterday and everything is still good.
I forgot to mention that while I was trying to fix this I eventually got in contact with Wacom Support. They only sort of help they could offer was useless. They recommended the following:
Thank you for contacting Wacom customer support.
Follow the steps attached and install the following driver:
http://cdn.wacom.com/u/productsupport/drivers/mac/professional/WacomTablet_6.3.1 5-3.dmg
* - The 6.3.15-3 driver may install on OS 10.12, but it is not supported under this Operating System. Customers may have issues with this combination that we may not be able to resolve!
which of course, I had already tried and did not work.
Anyway, while reinstalling software I suddenly got this message while installing a VPN:
It tells me I have to add the "Wacom Tablet Driver" to accessibility list in Security settings. Which to me seem kinda weird, why would a VPN trigger this with the Wacom driver? Also this also fits with the timeframe when my real trouble started happening. I installed the VPN last working day before Christmas and my trouble started first working day after Christmas. At the time I did not see that there could be a link between the VPN and the Wacom troubles. But now it seems more likely that there might be a connection.