drive cycle procedure says to use a steady foot. the whole break-in thing is kind of null and void if you didnt follow all of the directions to a 't'
at this point, if you want it fixed you need to take it to lincoln and let it be their problem. how many miles have you put on the car since you have been having the harsh tranny shifts? have the the shifts gotten worse/more harsh? have you had any other catastrophic failures <that you are aware of>? keep us updated with lincoln's fix(es). it has been about a year since you mentioned harsh shifting, and you alluded to it being an issue for some time before you posted, so over time you pretty much stress-tested your tranny, which most people do not have the cojones to do. <ha> i think your answers to these questions will be helpful to majority of the people here who are relegating the LS to a 'bang for the buck' daily beater and are not sure if they should bother throwing time & money & effort at shifting issues.
stress tested the transmission for about 40 000 kms since the harsh shifting started and now finally after replacing the solenoid pack and updating PCM and recalibrated shifting like new again these cars have solid transmissions