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Unfortunately, while IR thermometers are great, especially now that their prices have come down substantially, they don't read through glass. The temperature reading through the sight glass won't be accurate or of much value in giving the ninja's oil temp.
As for the thermocouple, it will work. The wire is very thin and flexible. While looking at your oil fill opening, the clutch basket is to the left. There's more then enough clearance for the wire to slide down the sidecover to the oil level. On your bike, the thermocouple will have no problem. In fact, this is the whole reason and purpose for their use, getting into tight, tough spots.
As a side, the wire will also feed easily into an auto dipstick tube. The wires are also usually supplied in 3ft lengths but just about any length can be ordered.
Doug
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