It might be difficult to get the probe section of a standard or meat thermometer in full contact with the oil. And while an infrared thermometer I'm sure would prove useful for a host of applications; one example is they are a crude but effective means of checking lean/rich carb adjustment by measuring temp of the header pipe BUT I don't believe it would work that well at measuring oil temp.
I would suggest getting a thermometer using a thermocouple wire that can be placed down the fill hole. I have two; one came as an option on a multimeter and another I purchased for datalogging capability - but this option is fairly expensive. I would suggest a simple thermocouple system as once you have it, you'll find all kinds of uses. I did a quick google and found a cheap one. There very well could be others cheaper and I make no recommendations about this one as I don't know anything specific about it but would highly recommend researching and getting one as I know it will prove useful with your intrigue in FE experiments:
Professional low cost Digital Multimeter with Temperature Function
I also would recommend sending an email to Watt-man at the KLR650 radiator-bypass link I gave earlier. He is a mechanical engineer and very knowledgeable about efficiency and correlation with temperatures. He's also a bike and auto enthusiast. While the lil'Ninja is noted for high FE, the coolant system of cyclic shocks of cold/hot/cold/hot ... predisposes this bike to accelerated wear and reduces potential of further, increased fuel efficiency. While Watt-man doesn't have anything specific for your bike, he would be a good person to seek advice on improving the coolant/temperature issue.