Hey, another who has seen this problem,
http://www.rangefinderforum.com/forums/showthread.php?t=37201
I think maybe it has not a great deal to do with the clutch or sprocket.
If your problem is the same as I have seen in a few of my FEDs, then it is probably due to the wind mechanism.
What happens is this: When you wind on (in a normal situation) the peg on the sprocket pushes the peg on the cog (facing the sprocket) round until the cog hits its end stops and thus stops the winder. The shutter tension is held in the winder by a small tooth at the base of the film spool shaft (see pic). The shutter button is pressed and the pegs are lifted apart, the cog has nothing to hold it back so turns back, the curtains do their thing etc, and the peg comes to rest in front of the sprocket peg (stopped by the other end stop acting on the cog). What happens in a my few examples is that, after the bottom cog is released, the sprocket advances fractionally so that when the cog is at its start point, it is no longer in front of the sprocket peg but on top or even behind it. When wound on, the sprocket peg must make a full turn (one frame) before it gets behind the cog peg again, then completes the wind, taking another frame to do so.
You can watch this happen quite easily, although it's usually an intermittent thing.
Why does it do this? Well, having suffered a great amount with my Zorki 6 with this problem, I think that I found the cause. As you advance the wind lever a small tooth latches into a cog in the winder assembly (you can see on the FED2 and 3 directly under the winder, next to the cog at the top of the wind up spool/clutch). In normal, well adjusted cameras, at the end of your winding-on, this tooth will hold back the winder tension quite comfortably, without allowing it to move. In a problem camera, the assembly has been wound just far enough for the tooth to drop over into the next trough (between the cog teeth), but not enough to drop fully down into place. When the tension is released (shutter button pressed) it is able to complete its movement and drop into place fully, thus moving fractionally, causing the mis-alignment of the pegs.
All this you can see, I would be very interested to know if this is the case with your FED3.
I think that the fix will be in the little catch tooth in the winder. Many of them (like the FED3) have a little slot which can be opened or closed, bending a small strip of metal which will (if closed) allow the tooth a little more movement. This tooth engages when the tension is released in the winder (when you let go) and allows the cog to return very slightly, this causes the tooth to engage in the cog. If the tooth were further away from the cog then it will stop the cog fractionally later and hopefully fully in position between two cog teeth. The attached picture shows the wind cog catch, you can see the adjustable slot. It's fairly easy to get at. I will be doing mine soon.
Just be sure, before you adjust anything that there is no debris lodged behind the tooth, holding it nearer to the cog.
Regards, Dave.....