My 01 yzf 600r idles at about 1200 when its warming up but once it gets to about 95 to 100 temp my idle jumps up to about 3 to 3500 and doesnt idle down is that normal?

The fuel / air mixture is lean. This means that air that has not gone through the carburetor is getting into the engine. Old rubber seals on the intake manifold no longer seal properly. The rubber may be cracked and letting in air. Potentially, a bad head gasket or a burned exhaust valve may be the cause. I would replace the rubber fittings between the carbs and the cylinder and that normally fixes the problem. If not, do a compression check to rule out valves / head gasket.

If the carb is adjusted correctly, the engine will not idle without the choke when cold. I will usually take at least 3 to 5 miles of riding to get the engine warm enough to idle by itself without the choke. If your bike is a full operating temperature, it should idle at about 1000 RPM. If it's idling higher than this, you need to slow it down a bit.

Remove the air filter cover and look at the top right side of the carb. You'll see a screw there . This is the throttle stop screw. Turn the screw counterclockwise to lower the idle speed to 1000 RPM or so. Blip the throttle and let it settle back to idle. Reset it if necessary. Once set, put the air cleaner cover hand on.

change fuel, change filter, if still happens get professional to check idle .

Sounds like you have blocked or partially blocked pilot jets,
this can happen if bike has been sitting anf fuel has gone stale in bowls or contaminated fuel in tank.
hopefully bike if well serviced or could be caused by air leaks or even tight inlet valve clearance if bike has done a lot of miles

you prob need a coolant temp sensor

Here is a diagram showing the tubes you connect your vacuum gauges to.
http://216.37.204.203/Yamaha_OEM/YamahaMC.asp?Type=13&A=326&B=11
The YZF600R is carbureted, so I do not know what you mean by throttle body adjustments.
Synchronizing carburetors means adjusting the throttle plates (butterflies) so that all cylinders are drawing the same amount of vacuum.
Here is a diagram of the carbs. Screw #31 is the screw used to change the sync.
http://216.37.204.203/Yamaha_OEM/YamahaMC.asp?Type=13&A=326&B=13
Remember one other key point, all carbs are sync'ed to the #3 carb. You cannot change the vacuum (directly) on #3. It is usually best to start by syncing #2 to #3, then #4, then #1. Changing #2 can affect the sync on #1 so you definitely want to do 1 after 2 no matter what. If you have one cylinder WAY out of sync, that would be an exception to the previous rule where you would want to attempt to get that cylinder in the ball park of the others before fine tuning each cylinder.
Syncing the carbs is an alternating process between adjusting the vacuum then adjusting the idle. If they were out of sync, bringing them back in, or even getting close, can cause the idle to raise because the engine isn't fighting itself anymore. Always keep the engine idling @ 1100 rpm's while syncing.

have you checked for heat damaged connectors from the alternator and voltage regulator? that is the common cause of this type of problem

all motors do this, its normal. once the bike is warmed up then set the idle where you want it.

idle adjust?
there SHOULD be an adjuster under the seat or gastank within easy reach. Clockwise to increase rpm, ccl to decrease rpm. idle around 1400rpm when engine is at normal operating temp. Good luck!