Are you sure that the oil spec is ATF? I've never had a wet clutch apart on a Yale, but on older Cat's & Clarks it's usually engine or hydraulic oil being sprayed. How much clearance does the disc have when the clutch pedal is depressed?

You say that it's worse since you've had it apart-how much wave did you put into the disc & how did you do it? The wave is there to help dampen engagement- not to force a seperation. Did you check the pilot bearing (or bushing) for clearance on the input shaft? On rare occasions with pilot bushings, I've had to have the trans in nuetral & set the parking brake & let the engine run for a while to get a bushing a little looser.