Update.
In order to make sure I did not miss any problem I removed the driveshaft, replaced rear flex joint (front one was fine), I also replaced the u-joint.
Then following this document AR41.10-P-0085-04A (use Google translate) I measured the drive-line angles and found that the most rear angle is out of spec by 1.5 degrees. I removed two spacers from under front differential mount - that brought all angles within specs and made almost a straight line between transmission yoke - driveshaft - rear end yoke.
Now I can say that if one drove the car, the vibration would never be noticed. I can feel it just a little at 40mph, but that`s more than likely coming from wheels and again - it is so faint that I am not going to worry about it.