Yeah, that's a weird one.  I would tend to think something is off with the clips as well.  Or, and I'm just thinking about something I saw recently with a hydrualic TO bearing, possibly there isn't any preload on the TO bearing?  My understanding is that there should be just a tad of preload.  Not enough to keep the tranny from going in, but enough so the TO bearing is lightly pressed into the fingers of the clutch cover.  I think the spec they gave was only like 0.005 or so for the hydraulic TO bearing.  I'd assume it should be the same for a regular TO bearing.  This would be easy enough to verify with some measurements from the bellhousing and block faces. 

Did you reuse your throw out bearing or install a new one?  

MS wrote:

Brand new Ford bearing.

There is preload since it is a cable clutch system. Holding the pedal down 1/4” makes noise go away, but if I adjust the cable tighter, the release point comes up higher than I want.

I am going to unbolt the cable and see if I can feel anything wrong with the release lever. If nothing improves, will have to pull the tranny.

   I know I pissed away a lot of time this last winter trying to get MDL hydraulic clutch adjusted.  I did add some preload and that made the difference for mine.  I also checked through the belhousing hole where the clutch lever went through to make sure there was no biding and everything was moving nicely on the transmission shaft.  I might just be a bad throwout bearing.  I cant think of anything else that would be making any noise in there but that. 
Steve69 
 

Steve69 wrote:

MS wrote:

Brand new Ford bearing.

There is preload since it is a cable clutch system. Holding the pedal down 1/4” makes noise go away, but if I adjust the cable tighter, the release point comes up higher than I want.

I am going to unbolt the cable and see if I can feel anything wrong with the release lever. If nothing improves, will have to pull the tranny.

   I know I pissed away a lot of time this last winter trying to get MDL hydraulic clutch adjusted.  I did add some preload and that made the difference for mine.  I also checked through the belhousing hole where the clutch lever went through to make sure there was no biding and everything was moving nicely on the transmission shaft.  I might just be a bad throwout bearing.  I cant think of anything else that would be making any noise in there but that. 
Steve69 
 

Steve - one thing to check would be to verify the clutch MC and the slave cylinder are 'matched', that is that when you operate the clutch pedal that you are getting full travel from the slave cylinder.  I have a external slave cylinder and changed to the MDL MC, and found I had to also change the slave cylinder to match as I wasn't getting full travel from the existing.  
 

Steve69 wrote:

BobE wrote:

Steve69 wrote:

   I know I pissed away a lot of time this last winter trying to get MDL hydraulic clutch adjusted.  I did add some preload and that made the difference for mine.  I also checked through the belhousing hole where the clutch lever went through to make sure there was no biding and everything was moving nicely on the transmission shaft.  I might just be a bad throwout bearing.  I cant think of anything else that would be making any noise in there but that. 
Steve69 
 

Steve - one thing to check would be to verify the clutch MC and the slave cylinder are 'matched', that is that when you operate the clutch pedal that you are getting full travel from the slave cylinder.  I have a external slave cylinder and changed to the MDL MC, and found I had to also change the slave cylinder to match as I wasn't getting full travel from the existing.  
 

   Hey BobE   I had the exact same problem.  I spent countless hours messing around with the slave cylinder MDL sent me and it wouldn't engage the clutch no mater how much I adjusted the linkage on the clutch MS.  They sent me a different external slave cylinder and that worked much better.  I had to also move the clutch pedal up a bit for more swing and some preload on the throw-out bearing.  MDL advised no preload on the clutch but that was the only way for everything to work properly.  Its working pretty well now.  We'll see how long it works before I have any issues.   My son and I installed the MS clutch cable on his 68 and that was pretty easy to install with the dash out and works well.  At the time I order the MDL system they didn't have the cable system for the 69 yet.  
 

I found I needed about 1.125" stroke.  Had I realized the MDL MC needed to be matched to the slave cylinder (my bad), I could have ordered the right size MC from MDL.  As the installation of the MC with the hydroboost brake system was a really tight fit required modified tools to tighten all the hardware, I decided to purchase a new slave cylinder from MDL.