Any advice would be most welcome.
Hi,
The long shaft from the clutch to the transmission stops turning when you push the clutch pedal down, so the shaft wouldn't make any noise when stopped.
It could be the clutch. If it makes a grinding, or metal to metal noise when you push the pedal all the way down, and you feel it in the pedal, the pressure plate finger height may be too low, and need adjusting, or raising up some, a common thing on Cubs.
If that is happening, the metal of the throwout bearing, or the throwout bearing holder hits on the turning pressure plate. Don't push the pedal down to where the noise happens, it can damage the clutch.
Below is a page from the 1947 Cub owner's manual showing adjusting the clutch pedal free play. There is a picture of the clutch lower on the page, you can see 1 of the fingers in the picture. There are 3 fingers. You have to get under the Cub, and look in through the hole under the clutch housing to see the throwout bearing, or fingers. Use a light. The hole originally has a cover.
The original style throwout bearing has graphite material, and doesn't turn. They can wear down from use. The material originally sticks out of the metal part of it 5/16".
https://farmallcub.club/rudi/farmallcub.com/rudi_cub/www.cleancomputes.com/Cub/Cub%20Owner's%20Manuals/McCormick-Deering%20Farmall%20Cub%20Owner's%20Manual%205-23-47/Page-40.jpg
IH changed the method of adjusting the pedal free play during 1948, so if your Cub is newer than that, it would be different than this manual shows.
Below is a picture of a new Cub throwout bearing.
