New clutch plate ?

Found the problem! Finally!

So, to review. The thrust washers fit perfectly, 0.002inch gap by feeler gauge. Throw-out bearing is perfect: no play, spins nice. Like new. I am in the process of putting it back together, and doing some cleaning as I progress. I realize this rub inside the flywheel housing - see photos. The pressure plate is rubbing the raised circular bump just below the crankshaft, inside of the flywheel housing where, on the other side, is the idler gear needle roller bearing. Why do I have this clearance issue is now the question. Sorry, I can't seem to drag photo into the post.

Yes - it's the most accurate way of doing it.
With the block on an engine stand and the crank vertical, you can use a prybar against a web to move it up and down.

let me get this right. Put a DTI on the end of the block and the gauge touching the end of the crankshaft to measure the end float?

Don't rely on the feeler gauge.

Clean everything up, and check the end float with a DTI gauge DRY - don't have any oil or grease in there as the reading will be wrong.

Engine is out of the car. Split the tranny. I cannot get the smallest feeler gauge between the thrust washers. I pulled the middle mainbearing cap and the thrust washers only have a mild rub on them - normal wear. By the way, This engine sat for decades, but has very few miles on it.

So now I'm perplexed as to what the source of the growl. I'll replace the throw-out bearing, just because. Not all is lost. This engine always leaked, so I can fix that and give it a nice paint job. Sigh.

I have always followed Alex's advice on this. Purchased my mini with the thrusts in the pan, due to some machining error or other, would rather not go through all that again. 

Thanks Alex, Good to know I have someone to ask if I'm stuck. I grew up on VWs and knew to not hold the clutch in too long. "You're trying to push the crankshaft out of the case". True with most old manual trannys. I spent the day cleaning the garage, making room. Little cars can get quite large when to take them apart! Henry

The thrusts on a Mini crank are not pressure fed, they're lubricated by leaking oil from the centre main.

Starting the engine with your foot on the clutch (like a modern car with it's 'safety' feature...) is a dreadfully bad thing to do as there is effectively no oil on the bearing face.  With a heavy race clutch spring it is possible to wipe out the thrusts in very short order. 

Sitting with the car in gear and the clutch depressed at a junction, will do a similar thing - I try not to have the clutch down for more than 5-10 seconds without releasing it.

Good luck with the strip down - we're here with sage words of advice as you go.

I looked at it just now. Hard to say if moving. Only talking about a few thousands of an inch. But using stethoscope method (ratchet extensions touching that end of the block to my ear) I could feel it. Sigh. Tear down time. This will be my first. Any advice?

Could be the thrust bearings.

Watch the crank pulley as someone presses the clutch with the engine running - if there's something icky going on it will move in and out.

My '67 998 Cooper was running fine. Then a subtle groan was noticeable when I push in the clutch - engine running of course. It's getting louder. I've removed the clutch housing. Replaced the the throw-out bearing and the clutch spring plate. No effect. Again, it is noticeable as soon as the throw-out bearing touches the spring plate. Louder when I fully depress the clutch to shift. It shifts fine. Runs fine. But something bad is going on! I'm afraid the problem is much deeper - crankshaft? or trans? Anybody come across this?