The speedo gear (vehicle speed sensor, VSS) has probably lost its teeth. The PCM needs this input (as well as the output shaft sensor, OSS). Since the computer thinks that the car is stopped (no VSS) but the OSS is working, it is confused and has turned on the 'transmission warning light' = flashing OD light.
Just a suggestion but you might want to put the original speedo gear in and use a SpeedCal. The white speedo gear has very thin teeth that eventually get chewed up.
Your luck is running out. The computer thinks there is a problem with the transmission and it is going to go into "limp mode". This will allow you to remain mobile but with little power. I do not know the specifics but "limp mode" is supposed to be designed to allow the driver to get to a service place.