KNOCK in Trans area of IH Farmall 460 Diesel. PLEASE HELP.

I was discing with my IH FARMALL 460 DIESEL and a knock suddenly started. Not in the motor. Also, this tractor does NOT have the T/A (Tourque amplifier) on it. The knock sound seems to be coming from the transmission section toward the bottom, where the Counter Shaft is. We removed the belt pulley assembly and any covers over that area to expose as much as possible except the large plate your feet set on when your sitting on the tractor. Noise goes away if I push the clutch in, and goes faster and slower with the idle speed of the motor.
We don't think there are any teeth missing from a gear.
To remove the sound of the motor, we jacked up the one tire so we can spin the tire by hand to make the noise and we noticed that when the clunk or knock happens, it actually seems to lock or "bind" the gears for just a second and there is a keeper clip on a gear that is in the same place every time the clunk happens. If we use little force to spin the tire and go very slow with turning the tire by hand, what ever it is will actually stops the tire. Understand that to make it do this, we are not turning the tire very hard at all and very slow. If it binds to the point of stopping the tire, we can make it turn again by pushing harder on the tire.
Getting ready to crack the tractor in a few days. Also going to remove the deck plate over the differential / transmission section.
PLEASE HELP. ANY IDEAS WILL BE HELPFUL. If more information is needed, please email me and I will respond. Thanks for reading. TOD.

Is the tough spot at the same place each time you roll the wheel? Is it in time with anything else you can see or hear? If you block the clutch forward, & put the shift lever in a gear, does this affect the binding as you roll the wheel? Try to isolate between transmission shafts & differential/final drive areas. Sounds like either a bearing has a couple balls out, or there is something like a piece of foreign material in a gear tooth.

Like Brownie said and i may add that you may have broken a tooth on the lower contour shaft or maybe in the bull pinion . There is no cure in a bottle for this one as it is time to get serious and start tearing it apart , not a fun job forsure and if your luck runs like mine there will be a pile of parts on the floor and a empty case setting there before ya get to what is broke.

Hey Brownie 450, you sort of hit it right on the head. I removed the heavy plate that I call the deck plate(its the plate where your feet rest when your setting on the tractor. Anyway, I removed the deck plate so I could see in There with no restriction and I must say it is impressive how they used to do things. The problem is that a roller from a roller bearing fell out somehow, dropped slightly down into a gear and pitched it between the gear it fell out of and the one below it which cracked the roller. Either the big or small piece of the roller shot across to the 2nd and 3rd sliding gear and chipped a toothed out of the 2nd gear. Surprisingly, the chipped tooth in the gear is not the clunk. The clunk is coming from the bearing (or what's left of it) and with the roller that is missing, each time it comes to the same location on the shaft, it clunks. As it turns out, the clip or keeper ring I referred to in my original post is neither. Its actually the backer plate of the roller bearing that ended up being the problem. And, as a bonus, I could see it before I went through all the work of (unnecessarily) removing the deck plate. And another incentive to buy yet more tractors and claim I enjoy using them, that gear tooth that is chipped, costs about $620.00 plus shipping and was caused by a roller that probably cost.$.20. Gotta love it, LOL.
I really want to thank the folks who took the time to read my post cause I really needed some input. And I want to thank the folks who took the time to reply to my post and send me emails with suggestions.
As for my Tractor, I can't wait to get her back together so my wife can complain about how much it costs to run and how little we make with the crops we plant. So I need to get back to work. Until next time.
Thank you, living the dream in Northern Michigan,
TNT!

Tod, if you really like working on them, replace the bearing only. The chipped tooth may only make a ticking noise you can live with. See if a welder or machine shop can build up the tooth.