I seriously doubt they did anything out of 'spite'...but I am curious as to what they talked you in to to total $1200 when all you wanted was a $80 alignment. They could have knocked a wire loose/off, but since the trouble already existed before you went there, all the more reason to not think they did anything intentionally to disable your transmission. If your Lincoln has 120,000 miles, the transmission may be simply worn out, or has anybody simply checked the fluid? And unless the fluid is dark/brown and/or has a burnt odor, do NOT allow it to be flushed. If the fluid is a nice red, a flush will do more harm than good. It could be a simple transmission solenoid, all the way to end-of-life problem. Take it to a reputable transmission shop. And like Aamco's ads say, "Half the people that come in don't need a new transmission" or they could just say "Half the people that come in we stick them for a new transmission". For $1200 you almost could have gotten a good reman transmission, which is every bit as good as a new $3500 one. But back to this: Check the fluid before anything else. Check at normal operating temperature, on level surface, Running in Park. If low only add a pint at a time. Re-check.
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