I'm not sure why you glued the runners to the long aprons before glueing the aprons to the legs?
I actually don't glue in the drawer runners until the entire table is finished and I know the runners are aligned properly. I even made a table where the drawer runners were never glued down, they float in a groove in the back and on a half lap on the front.
I used the same runner assemble for this table:
This approach will never get you in your current situation.