Oh yeah, you totally have to worry about alignment whenever you mess with the mounts.
What do you mean by "bushings"? The standard Yanmar mounts at least for the 2GM.... that I'm familiar with look like the one below that ScottyT posted here at Sailnet, a steel frame with the rubber bushing inside. You might have different ones for front vs. back with different stiffness--the 2GM does.
They aren't all that hard to swap out, though I had to lift the engine a bit with a jack, but you do have to disconnect the shaft and then realign when you're done.
Why do you think they are shot?
2000 Beneteau 331
Northern Chesapeake Bay
Ambition is a poor excuse for not having enough sense to be lazy ~ Steven Wright