I have had the same problems I jumped the wire coming out of the cdi and it fixed all the problems
TORS stands for throttle override system. It is designed to shut off fuel flow if the carb gets stuck open. It can malfunction very easily wether it be from water or bad wires or whatever. When it malfunctions it thinks that the carb is stuck open and therefore is supposed to shut off the fuel flow by closing the slides. What holds the slides open is your idle setting which is why they can affect eachother. The reason It can affect your idle is because the TORS housing also is the idle housing. So if you cut the TORS wire it COULD change your idle a little bit. The TORS in my opinion is just a way of yamaha getting out of some lawsuits. Even though it doesnt work they can say they tried. If you have any more questions, fire away.
What are the benefits of removing your TORS?