They don't have to be "broken in", but as far as adjustment, they may be slightly twisted and causing a vibration. Try this:loosen the mount to frame bolts and the through bolt slightly. Idle the engine for a minute,then re-tighten the bolts. That should let the mounts fall into their natural position. Do the same for the trans mount.
You could also try spraying some penetrating fluid on the rubber exhaust hangars in case they have shifted position.
You could also try spraying some penetrating fluid on the rubber exhaust hangars in case they have shifted position.