Should you do an alignment if you replace a motor mount?

 

Changing the mount won't affect alignment, the adjustable links move the alignment. You could possibly put the mount in a "strain" if you just swap it out and torque everything down. Tighten the center bolt and the two mount to frame bolts snug then back off just a little so the mount can "float", fire up the bike and let it run so the mount can "settle" into its natural position. I just tighten them up while its running.