The FCR carburetor consists of 3 separate yet overlapping circuits that control the air-fuel mixture at different throttle openings. A circuit is the (emulsifier) air and gas path used to supply the air/fuel mixture at different throttle positions. The idle or pilot circuit consists of the pilot screw and the pilot jet (PJ). The pilot circuit controls the mixture at idle and up to about 1/8 throttle. The needle circuit consists of the throttle valve, jet needle and the needle jet. This circuit controls the mixture from ~1/8 throttle to 3/4 throttle. The throttle valve cutaway controls from ~1/8 to 1/2 throttle and the needle taper controls from about 1/4 - 3/4 throttle. The main circuit consists of the main air jet (MAJ) and the main jet (MJ). This circuit controls the mixture from ~1/2-2/3 throttle to wide-open throttle (WOT). There are excellent diagrams in all three of the Inspection/Adjustment section, the Engine/Carburetor section, and the Tuning section of the owner's manual. You need to look in all three sections of the manual to get the full picture.
There are a few other circuits that are important but these are not usually addressed during basic jetting for altitude and weather changes. These include the accelerator pump (AP), the air cut valve (ACV) which is found on the WRF & YFZ only and the choke circuit.
The AP provides a squirt of raw fuel into the carburetor venturi when the throttle is jamed. It richens the mixture to run best at lower speeds, yet allows a leaner top end for more over rev. This system has a jet called the leak jet which controls how much of the AP squirt is redirected back into the float bowl instead of into the carburetor.
The ACV prevents popping on deceleration and cannot be adjusted but it can be bypassed.
The choke system is used to start cold engines. Since the fuel in a cold engine is sticking to the cylinder walls due to condensation, the mixture is too lean for the engine to start. The choke system will add fuel to the engine to compensate for the fuel that is stuck to the cylinder walls. Once the engine is warmed up, condensation is not a problem, and the choke is not needed.
Carburetor troubleshooting is simple once the basic principles are known. The first step is to find where the engine is running poorly. Remember the throttle position, not the RPMs, determine which circuit is controlling the mixture. Ideally, you would select the main jet first, then the needle and clip position, and then the pilot circuit. If the engine is having troubles at low rpm (idle to 1/4 throttle), the pilot system or slide valve is the likely problem. If the engine has problems between 1/4 and 3/4 throttle, the jet needle and needle jet (most likely the jet needle) is likely the problem. If the engine is running poorly at 3/4 to full throttle, MJ is the likely problem. While jetting the carburetor, place a piece of tape on the throttle housing. Place another piece of tape on the throttle grip and draw a line (while the throttle is at idle) straight across from one piece of tape to the other. When these two lines are lined up, the engine will be idling. Now open the throttle to full throttle and draw another line directly across from it on the throttle housing. At this point, there should be two lines on the throttle housing, and one on the throttle grip. Now find the half-way point between both of the lines on the throttle housing. Make a mark and this will show when the throttle is at half throttle. Divide the spaces up even again until idle, 1/4, 1/2, 3/4, and full throttle positions are known. These lines will be used to quickly find the exact throttle opening while jetting. Clean the air filter and warm the bike up.
On any circuit, if it is too lean it will pop and snap. If on the stand for the pilot or needle circuits, you can hear these best with the seat off listening through the air box. These are most often heard on deceleration but are sometimes masked by the air cut valve. The air cut valve should be bypassed for proper jetting of the pilot circuit on the YFZ. If you hear popping, too lean. A bog can be rich or lean but if it is not accompanied by popping, it is probably too rich.