Ok, I'm going to take a wild guess at a few things. First of all, there is no such thing as a Skunk2 ECU. There are only Honda ECUs that are chipped by Skunk2. I'm guessing that your friend looked at the label on the side of the ECU and said it was an automatic ECU, and I'm willing to bet that the ECU has been converted to a manual ECU while it was being chipped. It's just two jumpers that had to be moved. I'm guessing it's not a real Skunk2 ECU either if it's an LS swap; there are a lot of fake chips out there.

Your problem is most likely sensor related. If the CEL is real, and it's not just a swap related wiring problem, then you need to get a new temp sensor. The ECU uses the temp sensor for a number of control-related decisions, so if the sensor is bad the ECU can make poor decisions. You've stated a very obvious problem, and it's a very obvious answer. Get a new sensor, and go from there. If that doesn't solve the problem, you've cleared the CEL and now you can actually do some real troubleshooting.