I had to repair some mount beams that were inadvertantly ground down unevenly, which is similar to the problem you have, the beams and mounts not meeting up evenly. What I did is lay a thick layer of JB Weld on the mount beam. Then I covered that with a piece of Saran wrap, then put the engine in place, running the mount bolts, well greased with anti-seize, through the plastic and pulled the mount bolts up snug. The next morning, the bolts came out fine, the engine popped right out and the mounting surfaces matched perfectly.