Rubbing or Rattling sound

The pilot bearing also stops spinning (somewhat) - when the clutch is engaged correct? Possibly it was damaged during first removal / first install?  

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Correct. But is the t/o bearing making a small amount of contact when disengaged? The thought I had was will the noise go away or change with just a slight amount of pressure on pedal.
No, I actually measured a little over .200” clearance from the t/o bearing to the clutch fingers.

 
The pilot bearing also stops spinning (somewhat) - when the clutch is engaged correct? Possibly it was damaged during first removal / first install?  

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The pilot bearing rotates very smooth with no tight spots, it really feels good. I would think I could feel a bad bearing…… yes / no?

The rubbing sound makes more of an intermittent type noise like something is out of round, not the typical bad bearing noise. However, I suppose it could be resonating through the transmission. I’m going to pull the trans again next week (4th time) I will replace the pilot bearing just to totally rule it out, but I’m confident that’s not it.

This is a mid-engine, so I have done all of this moving the trans back about 8”, not a fun way to replace a clutch, I will probably have to totally remove the trans to replace pilot bearing.

Does anyone make a GOOD clutch alignment tool? these cheesy plastic ones are horrible !

 
The pilot bearing rotates very smooth with no tight spots, it really feels good. I would think I could feel a bad bearing…… yes / no?

The rubbing sound makes more of an intermittent type noise like something is out of round, not the typical bad bearing noise. However, I suppose it could be resonating through the transmission. I’m going to pull the trans again next week (4th time) I will replace the pilot bearing just to totally rule it out, but I’m confident that’s not it.

This is a mid-engine, so I have done all of this moving the trans back about 8”, not a fun way to replace a clutch, I will probably have to totally remove the trans to replace pilot bearing.

Does anyone make a GOOD clutch aligtnment tool? these cheesy plastic ones are horrible !
I have one - but I also have this shaft I just had to replace from my S5 - it can be used an input shaft....are you in San Diego? I don't want to ship it (too lazy). 

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I have one - but I also have this shaft I just had to replace from my S5 - it can be used an input shaft....are you in San Diego? I don't want to ship it (too lazy). 

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I’m in San Diego today & tomorrow, (Point Loma) I live in Corona, I can deliver it or ship it back from my business.

 
The pilot bearing also stops spinning (somewhat) - when the clutch is engaged correct? Possibly it was damaged during first removal / first install?  

View attachment 88984
Clutch pedal in, pilot spins. Clutch pedal out, pilot doesn’t spin. Seems it would be the opposite if the pilot was hosed. Same with thrust bearing problems. 

My assumption is it’s in the trans since everything else is new and same sound. Sounds like a dry bearing or something rubbing somewhere. 

 
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Mine was the pinion bearing. While driving (under load) noise got progressively worse. Foot off throttle (no load) noise would go away. 
trans out of car felt fine. With out video, they would have thought I was crazy.  Bad bearing let pinion float and destroy itself. 5500 rebuild 

I suggest send trans in, don’t drive it or repair bill will get bigger, lol

 
You should be fine, mine made a tick noise, First trip and had a bad pinion bearing,  

Then the tick went to a clunking noise due to the fulcrum from the bearing was in the teeth of the ring gear, think it was about $6000 after two trips,, 

I now supply my own Pinion and Main shaft bearings,  all from the Timken Dealer with Matched Races  

 
Update.

The sound is coming from the rear of the trans, if I push the reverse mechanism opposite the direction of going into reverse, the sound stops. This is with the shift cable removed. So I believe there is an internal adjustment that needs to be addressed. Anyone have experience with this ?

 
If it is all brand new with 0 miles, why wouldn’t u take it to the trans builder?

 
Because I’ve had it in & out 4 times, and I have discussed this issue with them. If it’s a simple adjustment, I would prefer to do it myself instead of pulling it out again and taking it to them. Obviously, if that’s what’s required, then I will do it.

 
Only adjustment on the outside of the trans that I know of is the brass bolt for the ring gear and slave cylinder. 
There are choices where to hook up the cable for forward gears but not for reverse. 

 
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This has been resolved,

The sound was coming from the reverse idler gear. I adjusted the linkage to push the selector shaft slightly past the detent. Easy fix!

Thanks to all who replied. Special thanks to Sean@weddle for technical support and wesinls for driving a 1/2 hr. out of his way to give me a input shaft instead of using the crappy plastic clutch alignment tool. 

 
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