The correct solution for the whole addition I am realizing now was to bulldoze it and start from scratch, however since that did not happen, every floor joist was faced with a clear (meaning a grade with only a few small knots) 2x6. After a half an hour of slamming the first one in place with large hammers and crowbars, Doug figured out that taking quarter inch notches from the ends of the joists made them fit without too much trouble, and the difference in height could be fixed easily with shims.
Once all the beams were up Doug had to run off for a few hours to volunteer at a prior engagement. This did not stop me from cutting out the hole for the new stairwell and making sure it was cleaned of nails and materials. I also decided to take a break a few hours into this endeavor when one of my boot laces became tangled up on a nail which in turn caused a miss-step through a gaping hole in the floor. I got off easy though with only a bruised knee. All things considered, far better than the other potential outcomes.