Whirring sound from transmission

Having an issue that I'm trying to pin down.
Truck has 18sp Eaton Autoshift. Clutch is about 1.5 yrs old...oilfield truck but mostly longer hauls on pavement.
Initially, we were having issues with the direct drive two way PTO. When trying to put it neutral...it would keep running and you had to play with the PTO switch to get it to kick out.
But the other night my driver tells me it's making a whirring sound as he's driving...also in neutral. When PTO is running...it sounds even worse. Almost a clacking and howling sound.
So he gets back and I pull the PTO. Gears on tranny look good...as well as the PTO. Tested it and air actuator on PTO is screwed up...so we install a different PTO....checked lash and was good.
Figuring the problem is solved.My driver takes it this morning and it's still making the whirring sound at idle.
As you push in the clutch...the sound goes away. When you engage PTO...it still sounds like a howling/scraping sound coming from the transmission/PTO area.
And when you disengage the PTO and truck is at idle....goes back to the whirring/growling sound.
I'm thinking maybe a release or pilot bearing in the transmission/clutch? Anybody have any ideas?

 

Backlash was set to spec at about .08. At first we re-used the gasket and checked but it was at 0.32 with significant play. So we put a thinner gasket and much better.
Gears on the PTO we took off were still in very good shape. And no adapter gears used.
So it doesn't seem like a PTO issue at this point. Two PTOs and same problem

 

Yep...sorry. add a zero to those numbers lol

 

Thanks...I'll check that out. My buddy did the actual measuring so I'm not sure.