Automatic gearshift not working

The 2 issues are probaly seperate. The tranmission issue is due to a problem in the valve body of the transmission. The manual/auto transmissions have a very complicated valve body that will cause havoc when the smalles thing goes wrong. It is not a surprise that since the manual shift does not work in all gears that the automatic shift does not work at all. The manual shift leaves less work for the valve body and other components to do inorder to shift the tranmission. For the automatic shift to work, every little spring and ball adjustment in the valve body must be workng correctly in synch with the sorrespong parts to shift the transmission.
If the emissions light goes off after a few seconds, the issue is probably not that bad yet as it is slowly failing. It may even be the proper sequence to check the emissions system when starting the vehicle as the light staying on or not coming on at all can be a sign of a problem in some vehicles.
The best thing to do first is to have the trouble codes pulled and that will give you a start as to the source of the problem.

It may be the TCM, but the shift solenoid may be at fault as well. There are 2 solenoids for the first to second shift. The shift solenoid and the conveter solenoid. If the converter solenoid is bad it usually causes a, "Shudder" that you can feel. To test the shift solenoid, I do not have the location but I will try to find it if you need it, put 12 volts to the solenoid and see if it moves. Also check the passage for blockage. The fact that the manual shift does not work suggest this may be the issue as it should overide the TCM, not sure about that with the failsafe option. Testing the TCM is a pin by pin test and I don't have the pin out for it. If you know of an American counterpart, I may be able to find it, nut I usually don't have pinouts or the tests for them. You will have more luck finding them on the internet. It is usualluy a simple voltage test. However the TCM can be shorted out and a voltage test is risky, so I would test for continutiy checks if you can find them. Apower distrivution wiring diagram will work best for that.
I think the first and easiest thing to do is to have the trouble codes pulled. It takes less than a minute so most repair shops will do it for free or next to nothing.