Place the probe about one inch from the flange with the tip of the probe in the center of the flow. It's not real important. The readings you get, are the readings you get.
There is no high limit on the EGT temps. What will happen, if you go too lean, the temp will reach a peak and then it will go down. Sneak up on it. This can happen on the low-end too. Sometimes, at peak torque, the engine can go lean just like on the top. If it does this, go bigger on the low-speed jet. If the clutch locks up, causing a drop in RPM, it's been my experience that the carb needs to be richer on the low-speed needle.
There is no truth to the rumor that you're going to melt the aluminum if the EGT goes too high.
What can happen is the EGT will reach a peak and then go down, that means you're lean and you could possibly melt the piston. Melting the piston will not happen instantaneously with a drop in EGT, you'll have time to let off and head for the pits. Whenever you see the temperature lower than normal, always go richer first. If it goes lower still, that tells you it was lower because it was rich, not because it was lean. It takes some getting used to.
As far as the probe blocking the exhaust flow, I would love to see the data verifying that it causes a loss in power.
There is no perfect temp with the EGT. It will change with the compression ratio, the air density, maybe the cam and maybe the spark plug. Take some time and figure out what the ideal EGT is for your setup. One piece of advice, get an air density gauge. With a two cycle, because of the adjustable carburetor jetting, you can adjust on the fly, but with the fixed carburetor you're using, you need to anticipate what jets you should have in the carb before going out on the track.
Comments compliments criticisms and questions always welcome.
If the data does not support the theory, get a new theory.(Al Nunley)