This is a way to save yourself some money for when your FZR neglects to shift, misses shifts or slips out of gear periodically. This is where trial and error took me. So I took notes and documented it for you all to use.
PAY ATTENTION: Cross reference these factors and see if they apply to your bike...
Symptons: The bike would not shift in to or get in to second gear. Only went into 1st and Netral Sounds, Noise, Etc...
The bike may not always present a noice. In this case, the "clunk" or grinding shift was not present. There was simply no second gear at all....
Possible Culprits: Shift shaft, Shifter Forks, Or a destroyed 2nd gear. According to Mark, the tranny gears may not display any damage at all. Its the shifting units that get the damage.
How mush did it cost to fix and where from?
Bike Bandit (http://www.bikebandit.com) prices are:
shift fork shafts are around $12
shift forks are around $35
shift cam or drum is about $100
the shift shaft is about $47
Many problems can be directly related to the previous statement. It is always best to start with the easiest solution first such as:
Clutch cable
Improper oil level
A lead foot and so on
If that does not work- Here is where the fun begins...
The processes of removing/replacing shift forks, shift fork rods, shifter shaft and shift drum within the transmission case can be completed with the motor in the frame. With a small portion of patience and precision total time from start to finish can be accomplished in about two hours.
Tools (most common to use)
1.#5 allen wrench
2.10mm socket and wrench with an extension
3.12mm or 13mm deep socket
4.Allen wrenches to remove body work
5.Two fingers of The Glenlivet
Steps:
1.Remove the tail fairings and side panels as well as the tank cover.
2.Remove the exhaust from the headers down.
3.Remove or move out of the way from the carburetors the fuel tank.
4.Drain the carburetors from the float bowl drain screw.
5.Drain the oil. There will still be residual oil in the case that may cause a big sloppy mess.
6.Remove the clamping bolt securing the shift linkage pivot boss to the shift shaft and let it hang free. (the part where you shift with your foot)
7.Remove the clutch cover. When that is off, unscrew the 5 pressure plate screws that secure the clutch. Make a mark on the top of each friction plate so you can put them back in the right order. (see illustration below)

Once removed you will see this

8.Pull out the shift shaft and inspect it for straightness or other damage and you will see the shift drum and the corresponding “gears”
9.NOTE: Shift fork shaft “A” should be metal and “A” and “B” will have a tab that you will need to remove to get the shaft out.


10.This step you will need to lay the bike down on the left side (riders left) I would suggest a soft pad near where the stator cover will sit so you don’t scratch anything. This part is hard to look at but easier then taking the motor out. I did it both ways.
11.Now you see the bottom of the oil pan,

12.Remove the fourteen allen screws and take the pan off. The screws are all the same so don’t worry about the order of them.
13.This next picture you can see all of the internals after you remove the oil pan. There are three shift forks: right, left and center. These forks will move along the shift fork shaft when you manually shift gears and line up the gears of the transmission. Remember where they go for an easier time to put it back together.

14.Remove the tabs that secure “A” and “B” in the clutch area and then remove the both shift fork shafts. They are different so make a note.

15.Now move the shift forks out away from the shift drum in order for the drum to be removed and move the stopper lever away from the star shaped gear on the shift drum.

16.slide the shift drum out of the engine case. Remember what Gear it was in for the reinstall. Check for strange or uneven wear, if present replace. Now you can see the shift forks.

17.Pull the shift forks out and remember where they go. They should only go in one way but just to make sure. Inspect and replace if bent or broken. While this is all out inspect the internal gears and the shift dogs (see illustration)

18.here is everything that you should have out. Any one of these could be bent or broken to where we can barely notice, but the bike will notice, so if anything just doesn't look right, replace it or it can cause more damage down the road.

to reinstall put the shift forks in first and follow the above in reverse.

Again this can be done with the motor in the bike and I would think most average mechanically inclined people could handle this quite easy. I hope this makes sense, its getting late Good luck.
Permission granted to FZROnline.com by yammyha to post this thread in its entirety.