Clutch release fork not lining up with hole for slave cylinder
 

I tried replacing my slave cylinder but throw out fork did not line up with the push rod correctly and I destroyed the first cylinder trying to bleed it on the transmission. I then took some pictures of the inside of the transmission and saw that the throw out fork is not centered on the hole.
http://rocbyter.freeshell.org/pics/throwOutFork.JPG
I tried to use a screw driver to see if the fork was movable but it didn't seem to want to move. I assume that this fork needs to be centered. The bad cylinder had a rip in the rubber boot. I believe this was caused by the fork not being centered. Does anyone know if there is a way to move this and would it require the transmission to be removed. I hear that the throw out bearing does not usually go bad and am not sure if this would even cause this. Could this also be caused by the ball pin or spring clip? Oarts 6 and 7 on the image.
http://realoem.com/bmw/thumbs/s/f/14.png
Finally are there any tricks to getting the push rod to line up with the throw out fork. Even if it was centered it still seems pretty far in there? Thanks.

I would try to use a magnet and pull the visible end of the fork towards you as far as it will go. Then try to rotate the fork into proper alignment. The only way it could get like this would be for the other end of the fork to have come off the pivot (ball pin, #6). But the ultimate question is did it come off during the slave swap, or did the plastic pivot fail causing all of this?

If I'm envisioning the innards correctly, pulling the slave end of the fork rearward will push the opposite end (pivot end) forward, off the pivot. When you rotate it you will be trying to match up the pivot with its dimple on the fork. The fork has a dimple on the pivot end just like the slave end.

If you can get the pivot end matched up, I'd put forward pressure on the slave end with a Phillips screwdriver or something like that. Ir maybe even your finger. While you are holding forward pressure, try rotating the fork clockwise (like it is now) or counter clockwise. If it still rotates I'd guess the plastic pivot failed.

I hope that all makes sense :)

I'm with CirrusSR22. You can TRY to get it all back together, but I'd suggest a bright light and a small mirror to try and see what is going on in there.

I do suspect the arm is off the ball, the ball is broken, the arm is bent or a combination of all of these.

I also suggest pulling the tranny because most likely the clutch is close to the end, and any damaged parts could cause other parts to fail (such as the throwout bearing) so pull it down and check it carefully and completely.

Thanks
 

Thanks for the advise. It looks as though the transmission will need to come out or at least the bell housing. I don't feel that I have the skills to do this in a reasonable time frame so I'm having a trusted mechanic finish the job. On the bright side I'll have an excuse to replace the transmission mounts at the same time.

Turns out the issue was with the ball pin part 6 in the diagram. Your correct J!m the ball was broken. I had to have this fixed by taking it to a transmission place being that it was beyond my skill level. The transmission had to be removed to fix this issue. I payed $430 in my area and it was the best price I could find. Hope this helps anyone having a similar problem.