Having just been through a four month issue with running gear ourselves it is easy to envision the possibility that the additional load your engines are seeing was caused by actions the yard took to correct whatever your initial problems were. This could have resulted in increased friction due to misaligned engines, misaligned struts, incorrectly sized cutless bearings, bent shafts, shaft couplers not properly aligned with the shafts or mated to the transmission output flange, improper clearance between the shafts and the insides of the packing glands, bent shaft log hoses, or something else putting enough pressure on the components to increase the drag and thus the load on the engines causing them to work too hard, hence your black smoke.
Our situation had nothing to do with alignment or engine load but I know how easy it can be for several things to change when one thing in the system is changed or worked on.
You mention the yard found problems with your "struts and driveline." Does this mean both sides or just one?
Do you know if your shafts were easy or relatively easy to turn by hand from inside the engine room before, and if they were, are they still that way? If there is no change in the effort needed to turn them, that does not mean that misalignment of some sort is not the culprit. But if there is a difference in the effort to turn them that can be a clue that misalignment of something could be the problem.
Unless you had the props worked on they should be the same as they were before your haulout. And if they were clean when the boat went back into the water it would be surprising if both of them got fouled enough (depending on how long it's been since your haulout) to have such a severe effect, although with boats one soon learns to never say never.
Black smoke notwithstanding, does the boat feel like it's doing the same speed and going through the water in the same way at the same power settings now as it has in the past? Don't know about your boat but when ours is nearing the need for a haulout with significant bottom, prop and rudder growth we can feel the difference in the hull's movement through the water, to say nothing of seeing it on the knotmeter.