Hey i did a auto/manual swap just befor winter and the clutch seems to not engage and disengage completly, its very weird cuz if i drive for a little while it works fine but after its been goin for a longer time it grinds 3rd occasionaly, what can cause this? i have a new master and slave. theres no leaks, bleeded the hell out of it. But on the pedal there is alittle spot where nothing happens, its right at the top, what im trying to say ther is that when i push the pedal for the first few cm i feel no pressure, i think the spring on the assembly might be lose. could this affect how the clutch works ? i was planing on doing a full SS set up from master to slave to see if that would help but im not to sure it will if the pedal feels worn out.
Maybe your pedal adjustment? i just had mine swaped too, i dident have the problem you are having but maybe thats what is wrong here too.
this was mine…
http://www.son240sx.ca/forums/showthread.php?t=26236
Good luck fixing it 
I’ll try that, hopefully that works