it listed 2dr hatch 2.4L 4CYL 4A and 2dr hatch 2.4L 4CYL 5M
and also spec 2dr hatch 2.4L 4CYL 4A and spec 2dr hatch 2.4L 4CYL 5M
...anyone know the differences between these fours?

l am guessing the difference is in the options. You need to check them out in person.

The spec edition is Scions ''tuner'' model. For about 1200 bucks less, u lose the alloy wheels & the sunroof. The glass is still there, it just does not open up. There r numerous other things that r deleted that do not really mean a lot, like engine cover, cruise, auto up & down windows (tc has one touch operation, spec does not), urethane steering wheel instead of leather. There r few other things l can not recall off the top of my head, but those r the biggies.

To me, it is not worth it to go with the spec. the idea of a spec model was sound, but the execution left a lot to be desired.

The primary difference between the 4a and the 5m is Automatic trans or Manual 5 speed trans