Maybe it's the years (decades) of commercial/industrial sheet metal work that helps me understand things don't need to line up perfectly to work out just fine. That's what clamps, jacks, drift pins, chain hoists, pry bars, and such things were made for! I see nothing you've shown that would deter me for a moment, but I will admit to a heavy handed approach when need be. Main thing is that the bracket is tight to the frame on both the side and bottom before marking and/or drilling the holes, using whatever methods required to make that happen. The last picture I'd clamp the bottom of that bracket to the frame, draw it up tight, take a 12mm bit, run it up through the bracket, and drill enough of the holes to get centers located. The urethane bushings in the cradle will give enough to allow slight misalignment issues, you can turn the bolts in and let the threads pull them in if you can get them started into the mounting holes.
Jay