1998 Chevy Cavalier 2.2L Theft Mode Issue

Ok here's what happened I was coming home from work one night and had to go through somewhat high water. The car went through the fine did not shut off stutter or anything similar.

The next day when I went to get in the car the fan was running and the car was off we did try replacing the relay no luck it would still turn on randomly with car off. We did try another fan which was known to be good same issue. We ended up wiring the fan directly to the windshield washer fuse and that issue corrected itself.

Now my issue is this when the car sits for 2 hours or more it goes into a theft mode like state. I have to leave the key in the on position after 1 or more failed starts and when I hear the fuel pump kick in turn the key and i'm good to go. One other oddity the check engine is always on and on the dash where you gear is indicated by an orange light most of the positions don't light up since the water incident. Car drives fine all gears work. I've noticed that when I get it to start the first time the theft mode will stay on if I turn it off then back on the light will go out and check engine stays on.

I'm thinking it's the computer. Anyone have any other suggestions?