Unfortunately the EPA considers any problem which causes the check engine light to turn on, a smog check failure. We realize the problem your Ford Taurus is facing is only transmission related, however since the Check Engine is illuminated it can not pass the smog inspection.
Your option in this case is to have the transmission fault repaired. You may consider applying for the CAP vehicle repair program which will pay up to $500.00 toward your Ford's smog check repairs.