Not shifting

1996 Mazda 626, automatic transmission, with 166771 miles. I had a new motor put in 9 months ago. The Stupid mechanic didn't replace the front seal on the transmission so I had that replaced about 2 months ago. It was running fine for awhile but for the last week when it gets to the normal operating temp. It doesn't want to shift out of second gear. My check engine light is on and when I start it up and drive after I have driven about 5 miles my over drive off lights starts to flash. Any ideas on what is causing this? I'm lost. I have tried manually shifting it and that doesn't help either.