1994 Mazda Protege Recently Had Transmission Rebuilt Automatic Since Car Been

I recently had my transmission rebuilt (automatic) and since then the car had been driving basically fine. The shifting of gears seems to be timed very well, though they can be a bit hard when the car shifts up. Recently, my Check Engine light and Brake Light in the dash have been intermittently coming on and off. Yesterday, while parked at work, the RPMs went up and down a bit, and it felt like the car tried to shift gears and the Check Engine light would come on, then go off, then come back on each time it felt like it shifted gears. This is when I was in park mind you. I tried to use an OBD scan tool to get any codes but my Mazda doesn't have a place to hook it up to. Any ideas what I should check first? The oil, transmission, and coolant levels are all full.

For the Check Engine light, I have noticed that as I am coming to a stop, the RPMs jump about 100 right before I reach my Idling RPMs at about 1000. Also, I have started to lose power to the engine while driving a few times, I had to let off and repress the accelerator to keep from stalling out. Any help is very appreciated!