I have stumbled upon something that mostly solves my particular problem. I always liked Safari to open on my secondary display but haven't had any luck since upgrading.
I opened Mission Control and added a new desktop to my secondary display, (desktop 3). After that, a context menu came up when I right-clicked on the dock icon for Safari, it allowed me to use the 'Assign to' menu which was not previously showing up.
I could select 'Assign to Desktop on Display 2' and it will now open on my secondary display no matter where the dock is when I open Safari.
Remembering the exact position of the Safari window doesn't seem to work properly. If I move it to my primary display and close it, it remembers the 'relative' position but opens it on my secondary display... strange behaviour, but I am closer to my desired behaviour than before.
edit: it gets worse.. each time I open the application, it moves further to the right until it is butted up against the edge of the display..
Aye Caramba..