I think I got it fixed.
I unzippped everything directly into the game (instead of copying over the unzipped files from a temp folder) overwriting everything in the install.
The game then reached the mainscreen and would crash immediately.
I went into JSMGE and applied the DBW widescreen patch.
This seems obvious to some but I, and perhaps others who had UP3 running for a while before installing Dark Blue World might miss. My config.ini still had a widescreen aspect ratio and I did not think about that. The DBW instructions tell you to deactivate all UP3 mods,one of which is the UP3widescreen mod. When I tried to run DBW I did not think to apply the DBW widescreen mod before running DBW.
Problem one solved.
Problem two: the game still crashed.
My .exe switcher still had the 6DOF/trackir enabled from my UP3 install. But again the 6DOF mod from DBW must be applied before running with TrackIR or the game will crash.
I did not catch this at first since when i ran the game after fixing problem one, I did not have trackir running nor my HOTAS, because I was only trying to get the game to run, not trying to actually play.
So now everything seems to work (so far)