Sounds like your transmission is going to kick the bucket real soon. Not going into gear is transmission related not computer caused. Better take it to another mechanic, and look into getting a rebuilt one should be around $1000 or if you want to get a used one it would be hundreds less. Also I have heard that the transmission that Ford sells aren't that expensive considering the Warranty you get with it.
Good Luck.
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Richard
1995 Lincoln Town Car Signature Series
Past
1992 Lincoln Town Car Cartier Designer Series
1992 Lincoln Town Car Executive Series
1990 Lincoln Town Car