Jetting can make or brake your sled. If its jetted wrong and running lean you can melt it down before you realize it. Have you pulled the carbs and checked what Main Jets, Pilot Jets, where the Needle sits and where the Fuel screw is adjusted too? The numbers on the jets can be a little hard to read but if you can let me know those I can give you a rough idea of what it's set up for.
I've got the jetting chart for 98SRX as that's the sled I'm running and can get those on Tuesday when I get back home. It takes into account Elevation and Temp so if you can give me those for where you will be running I can let you know what the jet chart shows. (Someone correct me if I'm wrong, but if you jet for a lower elevation when you are running at a higher elevation it will be running richer. You're safer doing that so when you are at the lower elevations your not running lean.) Mines jetted for 3500-5000 at 20 degrees. I mostly ride about 4400-6000, but I have been playing with jetting still and checking piston wash/plug coloration. The chart isn't a fool proof method as nothing is in life, but gives you an idea of what to expect and where to start. The SRX runs a larger jet on the pipe side carb as it tends to heat up easier to from what I've been told and the chart shows that.
You also mentioned that your pipe is cracked, this could affect the carb jetting and you may want to fix it soon (or maybe I'm over paranoid). If the pipes are not the stock tripple pipes then jetting may be different too. I may have the clutching chart to give you an idea, but clutching is something you can play with and adjust until your blue in the face and not be satisfied with.
As for overheating there is a lot that can cause that. What is the temp light doing? The light will flash 3 times on start up then depending on how many flashes will tell you other things like the powervalve servo motor is not working but I do beleive will be on solid if your running too hot. What else is the sled doing and how long does it take to get hot? Hopefully I can be of help and have made sense. There are also some other sites that have great information on Yamaha sleds only. They are older and heavy sleds but set up right will run forever.