Scott,
What kind of rod-in-tube pushrods are you using? The Great Planes ones with the little white 'things' you slide on the rods don't flex all that much. If you secure them at each end and two places in between you'll be golden. And as stated above, do try to keep them straight.
The MDS has a cracked carb mount? Where it fits into the case?
JB Weld it! It'll be good as new. I have an engine that I burried 10 inches in hard dry ground. Half of the carb mount on the case itself broke off. I oiled up the carb and paisted the JB in the cavity-after thoroughly cleaning it first. A little RTV Blue to ensure a good seal and its good as new.
Put an APC 10X6 on the .40 and an APC 11X6 on the .46.
BTW, the best .46 for the money and performance is NOT an O.S. FX. Thunder Tiger Pro .46 wins that race. Cheaper too!

Jeff