2003 Kia Spectra '03 Kia shifting troubles

Transmission problem
2003 Kia Spectra Automatic 112000 miles

My Kia was submerged to the top of the wheels in a flash flood last week for a few hours. I let it dry out and then started it and there were obvious problems such as the car not idling properly. I drove it about 15 miles to my house and let it sit on an incline for a few days to dry out the inside. Then I drove it to the shop with no apparent problem except for the check engine light being on.
They said I needed a new Powertrain control module for them to figure out my check engine codes. I obtained one at a salvage yard and they put it in and also replaced spark plugs. They then told me I could come get my car and that it was running pretty good. I paid 377 dollars and got in my car to drive away.
The check engine light was still on and as I drove out of the shop I found that my car won't shift into 2nd gear until I reach 5000 rpms! And then again not into third until just over 4000 rpms! It also seems that the rpms have to be higher than usual to maintain speeds.
Should I take it back and have them tell me what the check engine codes are or is there a better course of action?