Since there are no specs to go by, where you take the temprature may be less important than consistantly taking the temp at the same location each time. With the small size and quick heat transfer on these engines, seems to me that the temp at any given spot will vary at an equivilent ratio. On the other hand, if on day you take the temp at the back of the cylinder with the cowl off, and then try to compare it to a temp of the front of the engine with the cowl on, then next time at the exhaust, there can be no meaningfull comparisons.

Scott