Start first by looking at the condition of the EVAP lines going from the intake plenum to the right hand fender well. Replace if dry rotted or cracked.
The purge flow sensor is located in this same line. The purge flow sensor fails at a very high rate. It's cheap enough to replace for trouble shooting purposes.
If the problem continues look for a vacuum leak at the charcoal canister and further down towards the gas tank.
Also check the filler neck for rust through and the gas tank filler neck grommet for rot.
For the blinking transmission light, the Ford service manual states:
Transmission Control Switch and Lamp Operation
"EPC circuit shorted (lamp flashing) or monitored sensor failure"
2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.