You will most likely need a stiffer rear spring if you want your sag to be right. Give Solid Performance over in Downingtown, PA a try if that interests you.
Do some searching on this forum and you will find many long and confusing posts on the TE mods. Here are my recommendatiosn after modifying my TE:
Aftermarket slip on. The stock can isnt super heavy but it aint light! There is a catalytic converted type thing in the stock can too which is very restrictive. You can go with a JD tuner for EFI performance but if I had to do it over again I wouldve gotten the Power Commander V. Also, you can send the ECU out to Zip Ty racing and have them re-map it to the "Map 3", which should alleviate any possible lean conditions or flame-outs not corrected by an EFI tuner.
Also I would highly recommend a Zip Ty Racing oil catch/breather mod. You could order one and have it shipped to you when they send you back your re-mapped ECU. With it, you can run "the correct" amount of oil (1150 cc's) in the motor and will not have oil seeping out of your airbox after the it blows out of the crankcase and into your airbox. This will also protect your torque limiter inside the crankcase, as it will bypass the hot crankcase gases up and out of the cam chain tunnel and into your breather instead of accross the torque limiter where it will possibly overheat that component. I am not trying to make you spend alot of money, specifically to Zip Ty, but they are very experienced with this model engine/chassis and the mods I have just listed will give the bike a very noticeable power increase and add years to your motor. Trust me, it is worth it. The bike will come up in the first couple gears and it will run cooler in the motor with more oil. Some guys have gone to a stainless steel oil filter and 0W wieght synthetic oils as well.
Other things...
Like any other bike, the factory doesnt throw a whole lot of grease on the bike. Check all the pivot points, ie, steering stem bearings, axles, suspension linkages, etc.
You can also flip the capacitor in front of the rear wheel upside down to keep heat/debris away from it.
I also moved my horn up behind the front light/numberplate because where it sits stock I was concerned with an impact that the horn would be driven into the right side radiator, not to mention the dirt and water from riding will fly right into the horn and kill it after a while (maybe I have OCD but I think it's worth doing).
Also, check your shifter and make sure its snug on the shift shaft.
If you ride this bike in the dirt you will see that it hooks up quite well with the CTS system. I was real happy with the bike. It's an awesome machine. Had to sell it to support my race budget on the WR300
Enjoy the bike and feel free to PM me if you need any help if you decide to do any of these mods.