Rep Power: 0

I drive a 2001 LX with a manual trans. It started overheating awhile back and I didn't want to mess with it so I sent it to a shop. A couple weeks go by and it's driving fine, until I notice the fans aren't kicking on and it starts overheating again. I cleaned the sensors on the radiator fan and they work now, but another problem arose. There was another leak in the coolant system. My friend and I decided to check one of the hoses connected to the firewall, so doing this we had to take out my air intake and unplugged the IAT sensor. We put some water into the radiator/reservoir and find the leak. We couldn't find it, so we decided to let the car sit since it was pretty late and just look the next day. Today we went to flush the water out of the radiator, and we noticed the IAT sensor was unplugged. We quickly blamed each other, then plugged in the sensor. Then I started the car, and the idle was shaking between 600 and 1200 RPM, and the CEL kept flashing when the idle fell, but would go right away. The battery light also came on. Confused, we turned the car off, unplugged the battery and the IAT sensor. I started the car and no battery light or CEL and it was idling fine, but the RPM gauge wasn't working. We plugged the sensor back in, and same exact problem. I'm extremely confused on what could be causing this, other than the IAT being plugged in could possibly be shorting out the TPS, but that seems highly unlikely. Either way, it got late again so I turned off the car and decided it was a tomorrow problem.

Any ideas on what the problem is/how to fix it are greatly appreciated. I am also a very broke college student with rent coming up this month so if this repair is going to be expensive let me know.

 
Rep Power: 225

You don't have water inside a bunch of connectors, do you?

You could also use a code reader to look at live data, see what the IAT reads.

Maybe check all the engine grounds as well. Should be one from the radiator support to the water block on the passenger side of the head. Another from about the same place to the battery negative terminal.

 
Rep Power: 0

I checked the IAT sensor and cleaned it out with caned air. I decided to try and do an idle relearn by disconnecting the battery/ecu fuse, reconnecting, turning it on and letting it sit for 10 minutes. after about two minutes the CEL stopped flashing and the idle was a lot smoother, but my RPMs won't show and neither will my temperature. I drove it around and it seemed like it was in limp mode, so i parked it for now. I'm guessing this is a problem with the TPS or just a dirty throttle body

 
Rep Power: 225

That sounds suspiciously like a loose alternator, I would recommend checking all the mounting bolts. There is one bolt on top of the alternator, one underneath holding it to a bracket, then another bolt underneath holding that bracket to the engine block. All need to be tight or it can cause issues similar to what you're describing.