shifter rattle

It’s not your throw out bearing. You have already checked your u joints. So let’s rule that out. Check your drive shaft slip joints for play, check your carrier bearing also. Tell me what truck suspension you have and truck model and year. This comes into play to isolate the noise. If you have air ride such as air tractor, there are wear plates. And at those miles, those plates will wear over an inch causing your pinion angles to be off a significant degree. So even if your joints and shafts are good, you will have angles off more than a degree

 

Reminds me of one that had balls missing out of the rear mainshaft bearing. Replaced that bearing and it worked great. An exchange is probably best.
It will not stand that bungy pulling on the stick, pushing the sliding clutch against the main shaft snap ring long.

 

Question?
Truck has 900,000 miles on it.
Have you changed the engine damper ?
They are Recommend to be done at 500,000 miles and can really make a difference.

 

My gear shift rattle was caused by Pilot Bearing/ So I replaced pilot bearing and input shaft and clutch fork

 

If you are worried you have bad shaft bearings in transmission like the guy you quoted, you would hear the marbles in a can pretty good while just coasting in first gear with a load on. Especially with a missing ball.
As far as dampeners go, that’s not what’s causing your shifter rattle. If it was, your dampener would have been so bad that the crank shaft would have trashed the main bearings within a mile and your motor would come apart. If you want a dampener anyhow, go with a vibratech

 

Typically Eaton transmissions don't use a lip-type seal on the input shaft. I believe its called a "wind-back" seal. I would guess that if its leaking, maybe there's excessive play between the input shaft and seal housing. That could mean a failing input bearing, kind of like what @BoxCarKidd mentioned earlier.

You could always try a plug swap (buy a 2nd drain plug and swap it with the old one). Then you might be able to see if there are any metal chunks in there.

Another option is to dump the transmission oil into a clean container and check for debris. Also remove the PTO cover and check bottom of the case for debris and visually check the gears. Only downside is you'll have to buy fresh oil to fill the transmission back up again if you need to take the truck anywhere. I'm not a big fan of re-using fluids if at all possible.