If the transmission filter was clogged, I'm thinking you'd see other issues besides the light.
As far as your code reader, I know some readers will spit out transmission codes, but that's not 100% every time. A higher end scanner might be able to see if there's any issues, but your mileage may vary.
With regards to these transmissions, everything I've heard points to them naturally running warmer than most transmissions, leading to the fluid eventually breaking down, and of course taking out the transmission. Since usually people aren't changing their ATF all that often, there's a good reason it's easy to find Taurii with dead transmissions with maybe 120-150K. A good rule of thumb is to do regular fluid changes on the transmission, maybe about every 15-20K. Adding a transmission cooler certainly will help extend the life of the transmission. Any licensed Mercon V fluid will work fine.