Did you swap the radiator too?
It is possible that if you kept the 1.3 radiator but didn't have it cleaned (assuming that you are lucky enough to have an older all-metal 1.3 radiator), it is possible that the radiator is causing your problem. Plastic radiators cannot be cleaned because most radiator shops will not mess with trying to disassemble the plastic units and then try to put them back together. Metal units are FAR easier to put back together!
The 1-wire temp sensor is very similar on both engines. I have used a unit out of a 1.6 engine on my 1.6 engine with a 1.3 head with some success - it didn't track perfectly but it worked okay. I also used a 1.3 sensor in it with success. I keep breaking off the wiring tab, then go to the pick n pull for a replacement from Samurais and TracKicks. That's how I found this out.