It looks like there are holes on the sides of the crossmember that bolt to the motor mount plates AND maybe one other hole at the very bottom of the motor mount plates that also bolts to a tab on the crossmember??
If so, I'd get some long bolts and loosely fit all of those lower bolts between the motor mounts and the crossmember, then see where you end up with the top of the framerail and the top of that motormount plate. Presumably, these parts were designed to work together, so MOST of the holes "should" line up.... if you are suspicious that the frame may be tweaked, deal with all the other ones first and see what it tells you once everything else is aligned and finger-tight.
-G