I removed this non-load bearing wall in the corner of my basement, now 2 doors upstairs rub on their frames. Why is this?
I really don't know where to start on this question.
There are several steps that need to be done, and soon before any serious damage is done. First, you need to stabilize the situation.  Several joists must be supported at once via a temp bridge support ( 2, 2X8's upright, spanning several joists)  held up by your temp house jack, but two would be better. One on either end.

Then you really should get the advise of a pro to evaluate your situation.  If you have a main lolly column sinking, that is a problem.  The 3/4 inch cuts should not be much of a problem, but they should have been made in the center of the joists, not an edge.  Are there any cracks traveling from these cuts? If not, then they are not the problem.  I have several theories, but without actually seeing the layout and taking measurements, it is impossible to properly evaluate.  Get a pro in there, don't take advice that is not based on an inspection of the problem.