Do you have a crane with spring scale? Lift up one side (SLOWLY!) with the crane until the weight reading is below some threshold, 1,000lbs, 2,000lbs? Whatever you feel is safe, crane still supporting enough weight to ensure you don't topple the thing over. Treat that as the tipping point, measure the tilt angle, and use trig to get the vertical COG. It will be as conservative as your spring scale threshold.
If you wanted to further reduce the chance of tipping, and increase the accuracy, you could plan to use the spring scale weight as part of the calculation. Modified method of the "tilt and weigh 4 corners" mentioned earlier. If you've got X,000lbs on the crane, X,000 on the ground, know the horizontal COG, and can measure the tilt angle, from there it is physics 101.
I'd like to think that this is a pretty elegant solution. Depending on the details it works out as the best option for accuracy, man hours (only thing quicker is a WAG - wild ass guess), engineering justification, and safety. You could eliminate ALL assumptions and peg the vertical COG dead on if you wanted, but as already mentioned, probably not worth the trouble.
I'd pull one side up with a spring scale until I had an appreciable angle and a clear change in weight distribution, then plug it in.
Because he is the engineering manager, not the shipping manager. And if this works out well he can write a procedure, this could be a chargeable item for a customer - dry and wet COG's verified.